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

Improved generic submissions to replace viral culture addition.

Browse Source
This commit is contained in:
lwark
2024-09-06 11:22:05 -05:00
parent bcb6e15449
commit 7f6a476cd7
11 changed files with 166 additions and 155 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
src/submissions/backend/validators/__init__.py
View File

@@ -26,11 +26,11 @@ class RSLNamer(object):
if self.submission_type is None:
# logger.debug("Creating submission type because none exists")
self.submission_type = self.retrieve_submission_type(filename=filename)
# logger.debug(f"got submission type: {self.submission_type}")
logger.debug(f"got submission type: {self.submission_type}")
if self.submission_type is not None:
# logger.debug("Retrieving BasicSubmission subclass")
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex())
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
if data is None:
data = dict(submission_type=self.submission_type)
if "submission_type" not in data.keys():
@@ -50,7 +50,7 @@ class RSLNamer(object):
"""
match filename:
case Path():
# logger.debug(f"Using path method for {filename}.")
logger.debug(f"Using path method for {filename}.")
if filename.exists():
wb = load_workbook(filename)
try:
@@ -70,12 +70,14 @@ class RSLNamer(object):
submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
case str():
regex = BasicSubmission.construct_regex()
# logger.debug(f"Using string method for {filename}.")
logger.debug(f"Using string method for {filename}.")
logger.debug(f"Using regex: {regex}")
m = regex.search(filename)
try:
submission_type = m.lastgroup
logger.debug(f"Got submission type: {submission_type}")
except AttributeError as e:
logger.critical(f"No RSL plate number found or submission type found!: {e}")
logger.critical(f"No submission type found or submission type found!: {e}")
case _:
submission_type = None
try:
@@ -112,7 +114,7 @@ class RSLNamer(object):
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
except re.error as e:
regex = BasicSubmission.construct_regex()
# logger.debug(f"Using regex: {regex}")
logger.debug(f"Using regex: {regex}")
match filename:
case Path():
m = regex.search(filename.stem)

4
src/submissions/backend/validators/pydant.py
View File

@@ -509,7 +509,7 @@ class PydSubmission(BaseModel, extra='allow'):
if check_not_nan(value['value']):
return value
else:
# logger.debug("Constructing plate name.")
# logger.debug("Constructing plate sub_type.")
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
output = "RSL-BS-Test001"
else:
@@ -642,7 +642,7 @@ class PydSubmission(BaseModel, extra='allow'):
# this could also be done with default_factory
self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
def set_attribute(self, key: str, value):
"""