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Code cleanup, dependency update, various bug fixes

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This commit is contained in:
lwark
2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
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17
src/submissions/backend/excel/writer.py
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@@ -31,7 +31,6 @@ class SheetWriter(object):
case 'filepath':
self.__setattr__(k, v)
case 'submission_type':
# self.__setattr__('submission_type', submission.submission_type['value'])
self.sub[k] = v['value']
self.submission_type = SubmissionType.query(name=v['value'])
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
@@ -40,7 +39,7 @@ class SheetWriter(object):
self.sub[k] = v['value']
else:
self.sub[k] = v
logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
# logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
if self.filepath.stem.startswith("tmp"):
template = self.submission_type.template_file
@@ -95,7 +94,7 @@ class InfoWriter(object):
self.xl = xl
map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, map)
logger.debug(pformat(self.info))
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, map: dict) -> dict:
output = {}
@@ -121,8 +120,7 @@ class InfoWriter(object):
logger.error(f"No locations for {k}, skipping")
continue
for loc in locations:
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
# 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)
@@ -152,7 +150,7 @@ class ReagentWriter(object):
try:
dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column'])
except KeyError as e:
# logger.error(f"Keyerror: {e}")
logger.error(f"KeyError: {e}")
dicto = v
placeholder[k] = dicto
placeholder['sheet'] = mp_info['sheet']
@@ -197,7 +195,6 @@ class SampleWriter(object):
def write_samples(self):
sheet = self.xl[self.map['sheet']]
columns = self.map['sample_columns']
# rows = range(self.map['start_row'], self.map['end_row']+1)
for ii, sample in enumerate(self.samples):
row = self.map['start_row'] + (sample['submission_rank'] - 1)
for k, v in sample.items():
@@ -229,8 +226,6 @@ class EquipmentWriter(object):
for jj, (k, v) in enumerate(equipment.items(), start=1):
dicto = dict(value=v, row=ii, column=jj)
placeholder[k] = dicto
# output.append(placeholder)
else:
for jj, (k, v) in enumerate(equipment.items(), start=1):
try:
@@ -258,8 +253,8 @@ class EquipmentWriter(object):
for k, v in equipment.items():
if not isinstance(v, dict):
continue
logger.debug(
f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}")
# logger.debug(
# f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}")
if isinstance(v['value'], list):
v['value'] = v['value'][0]
try: