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Troubleshooting.

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This commit is contained in:
lwark
2024-08-01 09:58:52 -05:00
parent ddf7937680
commit 88f3e92069
3 changed files with 75 additions and 39 deletions
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37
src/submissions/backend/db/models/submissions.py
View File

@@ -4,6 +4,7 @@ Models for the main submission and sample types.
from __future__ import annotations
import sys
import types
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
@@ -78,7 +79,8 @@ class BasicSubmission(BaseClass):
) #: Relation to SubmissionSampleAssociation
samples = association_proxy("submission_sample_associations",
"sample", creator=lambda sample: SubmissionSampleAssociation(sample=sample)) #: Association proxy to SubmissionSampleAssociation.samples
"sample", creator=lambda sample: SubmissionSampleAssociation(
sample=sample)) #: Association proxy to SubmissionSampleAssociation.samples
submission_reagent_associations = relationship(
"SubmissionReagentAssociation",
@@ -735,7 +737,8 @@ class BasicSubmission(BaseClass):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> 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
@@ -1633,7 +1636,8 @@ class WastewaterArtic(BasicSubmission):
input_dict = super().custom_info_parser(input_dict)
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 = [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
@@ -1641,7 +1645,9 @@ class WastewaterArtic(BasicSubmission):
# 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
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'] + 1)]
for datum in data:
if datum['plate'] in ["None", None, ""]:
@@ -1832,7 +1838,8 @@ class WastewaterArtic(BasicSubmission):
return input_dict
@classmethod
def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> 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
@@ -1846,11 +1853,14 @@ class WastewaterArtic(BasicSubmission):
Workbook: Updated workbook
"""
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)}")
if isinstance(info, types.GeneratorType):
logger.debug(f"Unpacking info generator.")
info = {k: v for k, v in info}
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):
source_plates_section = custom_fields['source_plates']
worksheet = input_excel[source_plates_section['sheet']]
start_row = source_plates_section['start_row']
# NOTE: write source plates to First strand list
@@ -1862,12 +1872,15 @@ class WastewaterArtic(BasicSubmission):
except TypeError:
pass
try:
worksheet.cell(row=row, column=source_plates_section['starting_sample_column'], value=plate['starting_sample'])
worksheet.cell(row=row, column=source_plates_section['starting_sample_column'],
value=plate['starting_sample'])
except TypeError:
pass
else:
logger.warning(f"No source plate info found.")
# NOTE: check for gel information
egel_section = custom_fields['egel_results']
if check_key_or_attr(key='gel_info', interest=info, check_none=True):
egel_section = custom_fields['egel_results']
# logger.debug(f"Gel info check passed.")
# NOTE: print json field gel results to Egel results
worksheet = input_excel[egel_section['sheet']]
@@ -1889,6 +1902,8 @@ class WastewaterArtic(BasicSubmission):
worksheet.cell(row=row, column=column, value=kj['value'])
except AttributeError:
logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
else:
logger.warning("No gel info found.")
if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
worksheet = input_excel[egel_section['sheet']]
# logger.debug(f"We got an image: {info['gel_image']}")
@@ -1899,6 +1914,8 @@ class WastewaterArtic(BasicSubmission):
img.width = 600
img.anchor = egel_section['img_anchor']
worksheet.add_image(img)
else:
logger.warning("No gel image found.")
return input_excel
@classmethod

7
src/submissions/backend/excel/writer.py
View File

@@ -173,11 +173,13 @@ class InfoWriter(object):
Returns:
Workbook: workbook with info written.
"""
final_info = {}
for k, v in self.info:
# NOTE: merge all comments to fit in single cell.
if k == "comment" and isinstance(v['value'], list):
json_join = [item['text'] for item in v['value'] if 'text' in item.keys()]
v['value'] = "\n".join(json_join)
final_info[k] = v
try:
locations = v['locations']
except KeyError:
@@ -186,8 +188,11 @@ class InfoWriter(object):
for loc in locations:
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']]
try:
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
return self.sub_object.custom_info_writer(self.xl, info=self.info, custom_fields=self.info_map['custom'])
except AttributeError as e:
logger.error(f"Can't write {k} to that cell due to {e}")
return self.sub_object.custom_info_writer(self.xl, info=final_info, custom_fields=self.info_map['custom'])
class ReagentWriter(object):

16
src/submissions/tools/__init__.py
View File

@@ -102,7 +102,21 @@ def check_key_or_attr(key: str, interest: dict | object, check_none: bool = Fals
if check_none:
match interest[key]:
case dict():
if interest[key]['value'] is None:
if 'value' in interest[key].keys():
try:
check = interest[key]['value'] is None
except KeyError:
check = True
if check:
return False
else:
return True
else:
try:
check = interest[key] is None
except KeyError:
check = True
if check:
return False
else:
return True