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Upgrade of WastewaterArtic parsers/writers for flexibility.

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This commit is contained in:
lwark
2024-07-09 13:09:27 -05:00
parent e589420815
commit 54e1e55804
11 changed files with 122 additions and 56 deletions
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5
src/submissions/backend/db/models/kits.py
View File

@@ -672,8 +672,8 @@ class SubmissionType(BaseClass):
Returns:
dict: Map of locations
"""
info = self.info_map
# logger.debug(f"Info map: {info}")
info = {k:v for k,v in self.info_map.items() if k != "custom"}
logger.debug(f"Info map: {info}")
output = {}
match mode:
case "read":
@@ -681,6 +681,7 @@ class SubmissionType(BaseClass):
case "write":
output = {k: v[mode] + v['read'] for k, v in info.items() if v[mode] or v['read']}
output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
output['custom'] = self.info_map['custom']
return output
def construct_sample_map(self) -> dict:

47
src/submissions/backend/db/models/submissions.py
View File

@@ -685,7 +685,7 @@ class BasicSubmission(BaseClass):
# Child class custom functions
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information
@@ -731,7 +731,7 @@ class BasicSubmission(BaseClass):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
"""
Adds custom autofill methods for submission
@@ -1307,6 +1307,7 @@ class BacterialCulture(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
@@ -1345,7 +1346,7 @@ class Wastewater(BasicSubmission):
return output
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information. Extends parent
@@ -1550,7 +1551,6 @@ class Wastewater(BasicSubmission):
return input_dict
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
@@ -1597,7 +1597,7 @@ class WastewaterArtic(BasicSubmission):
return output
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
"""
Update submission dictionary with type specific information
@@ -1608,16 +1608,20 @@ class WastewaterArtic(BasicSubmission):
Returns:
dict: Updated sample dictionary
"""
# TODO: Clean up and move range start/stops to db somehow.
input_dict = super().custom_info_parser(input_dict)
ws = xl['Egel results']
data = [ws.cell(row=ii, column=jj) for jj in range(15, 27) for ii in range(10, 18)]
egel_section = custom_fields['egel_results']
ws = xl[egel_section['sheet']]
data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for ii in range(egel_section['start_row'], egel_section['end_row'])]
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
input_dict['gel_controls'] = [
dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
data]
ws = xl['First Strand List']
data = [dict(plate=ws.cell(row=ii, column=3).value, starting_sample=ws.cell(row=ii, column=4).value) for ii in
range(8, 11)]
# NOTE: Get source plate information
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'])]
for datum in data:
if datum['plate'] in ["None", None, ""]:
continue
@@ -1808,7 +1812,7 @@ class WastewaterArtic(BasicSubmission):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
"""
Adds custom autofill methods for submission. Extends Parent
@@ -1822,30 +1826,33 @@ class WastewaterArtic(BasicSubmission):
"""
input_excel = super().custom_info_writer(input_excel, info, backup)
# logger.debug(f"Info:\n{pformat(info)}")
# logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
# NOTE: check for source plate information
source_plates_section = custom_fields['source_plates']
if check_key_or_attr(key='source_plates', interest=info, check_none=True):
worksheet = input_excel['First Strand List']
start_row = 8
worksheet = input_excel[source_plates_section['sheet']]
start_row = source_plates_section['start_row']
# NOTE: write source plates to First strand list
for iii, plate in enumerate(info['source_plates']['value']):
# logger.debug(f"Plate: {plate}")
row = start_row + iii
try:
worksheet.cell(row=row, column=3, value=plate['plate'])
worksheet.cell(row=row, column=source_plates_section['plate_column'], value=plate['plate'])
except TypeError:
pass
try:
worksheet.cell(row=row, column=4, value=plate['starting_sample'])
worksheet.cell(row=row, column=source_plates_section['starting_sample_column'], value=plate['starting_sample'])
except TypeError:
pass
# NOTE: check for gel information
egel_section = custom_fields['egel_results']
if check_key_or_attr(key='gel_info', interest=info, check_none=True):
# logger.debug(f"Gel info check passed.")
# NOTE: print json field gel results to Egel results
worksheet = input_excel['Egel results']
worksheet = input_excel[egel_section['sheet']]
# TODO: Move all this into a seperate function?
start_row = 21
start_column = 15
start_row = egel_section['start_row']
start_column = egel_section['start_column']
for row, ki in enumerate(info['gel_info']['value'], start=1):
# logger.debug(f"ki: {ki}")
# logger.debug(f"vi: {vi}")
@@ -1862,14 +1869,14 @@ class WastewaterArtic(BasicSubmission):
except AttributeError:
logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
worksheet = input_excel['Egel results']
worksheet = input_excel[egel_section['sheet']]
# logger.debug(f"We got an image: {info['gel_image']}")
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
z = zipped.extract(info['gel_image_path']['value'], Path(TemporaryDirectory().name))
img = OpenpyxlImage(z)
img.height = 400 # insert image height in pixels as float or int (e.g. 305.5)
img.width = 600
img.anchor = 'B9'
img.anchor = egel_section['img_anchor']
worksheet.add_image(img)
return input_excel

6
src/submissions/backend/excel/parser.py
View File

@@ -212,12 +212,14 @@ class InfoParser(object):
"""
dicto = {}
# NOTE: This loop parses generic info
# logger.debug(f"Map: {self.map}")
logger.debug(f"Map: {self.map}")
for sheet in self.xl.sheetnames:
ws = self.xl[sheet]
relevant = []
for k, v in self.map.items():
# NOTE: If the value is hardcoded put it in the dictionary directly.
if k == "custom":
continue
if isinstance(v, str):
dicto[k] = dict(value=v, missing=False)
continue
@@ -265,7 +267,7 @@ class InfoParser(object):
except (KeyError, IndexError):
continue
# Return after running the parser components held in submission object.
return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl)
return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl, custom_fields=self.map['custom'])
class ReagentParser(object):

10
src/submissions/backend/excel/writer.py
View File

@@ -8,8 +8,6 @@ from pathlib import Path
# from pathlib import Path
from pprint import pformat
from typing import List
from collections import OrderedDict
from jinja2 import TemplateNotFound
from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission
@@ -135,8 +133,8 @@ class InfoWriter(object):
self.submission_type = submission_type
self.sub_object = sub_object
self.xl = xl
info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, info_map)
self.info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, self.info_map)
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
@@ -154,6 +152,8 @@ class InfoWriter(object):
for k, v in info_dict.items():
if v is None:
continue
if k == "custom":
continue
dicto = {}
try:
dicto['locations'] = info_map[k]
@@ -187,7 +187,7 @@ class InfoWriter(object):
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']]
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
return self.sub_object.custom_info_writer(self.xl, info=self.info)
return self.sub_object.custom_info_writer(self.xl, info=self.info, custom_fields=self.info_map['custom'])
class ReagentWriter(object):