landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Second round of code cleanup.

Browse Source
This commit is contained in:
lwark
2024-10-30 07:34:39 -05:00
parent 1f83b61c81
commit ba1b3e5cf3
19 changed files with 176 additions and 110 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
src/submissions/backend/db/models/submissions.py
View File

@@ -6,7 +6,7 @@ import sys
import types
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
import logging, uuid, tempfile, re, base64
from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
@@ -167,28 +167,24 @@ class BasicSubmission(BaseClass):
"""
# NOTE: Create defaults for all submission_types
parent_defs = super().get_default_info()
# NOTE: Singles tells the query which fields to set limit to 1
dicto = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
dicto = dict(
dicto.update(dict(
details_ignore=['excluded', 'reagents', 'samples',
'extraction_info', 'comment', 'barcode',
'platemap', 'export_map', 'equipment', 'tips', 'custom'],
# NOTE: Fields not placed in ui form
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
'submission_object', "tips", 'contact_phone', 'custom'] + recover,
'submission_object', "tips", 'contact_phone', 'custom', 'cost_centre'] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover
)
# NOTE: Singles tells the query which fields to set limit to 1
dicto['singles'] = parent_defs['singles']
))
# NOTE: Grab mode_sub_type specific info.
output = {}
for k, v in dicto.items():
if len(args) > 0 and k not in args:
# logger.debug(f"Don't want {k}")
continue
else:
output[k] = v
if args:
output = {k: v for k, v in dicto.items() if k in args}
else:
output = {k: v for k, v in dicto.items()}
if isinstance(submission_type, SubmissionType):
st = submission_type
else:
@@ -198,7 +194,7 @@ class BasicSubmission(BaseClass):
else:
output['submission_type'] = st.name
for k, v in st.defaults.items():
if len(args) > 0 and k not in args:
if args and k not in args:
# logger.debug(f"Don't want {k}")
continue
else:
@@ -272,6 +268,7 @@ class BasicSubmission(BaseClass):
field = self.__getattribute__(name)
except AttributeError:
return None
# assert isinstance(field, list)
for item in field:
if extra:
yield item.to_sub_dict(extra)
@@ -1137,9 +1134,9 @@ class BasicSubmission(BaseClass):
limit = 1
case _:
pass
if chronologic:
logger.debug("Attempting sort by date descending")
query = query.order_by(cls.submitted_date.desc())
# if chronologic:
# logger.debug("Attempting sort by date descending")
query = query.order_by(cls.submitted_date.desc())
if page_size is not None:
query = query.limit(page_size)
page = page - 1
@@ -2980,7 +2977,6 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
Returns:
dict: Updated dictionary with row, column and well updated
"""
sample = super().to_sub_dict()
sample['ct'] = self.ct
sample['source_plate'] = self.source_plate