post documentation and code clean-up.

This commit is contained in:
lwark
2024-07-03 15:13:55 -05:00
parent 12ca3157e5
commit c460e5eeca
21 changed files with 421 additions and 238 deletions

View File

@@ -9,6 +9,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
"""
*should* allow automatic creation of foreign keys in the database
I have no idea how it actually works.
Listens for connect and then turns on foreign keys?
Args:
dbapi_connection (_type_): _description_

View File

@@ -1581,12 +1581,12 @@ class WastewaterArtic(BasicSubmission):
dict: dictionary used in submissions summary
"""
output = super().to_dict(full_data=full_data, backup=backup, report=report)
if report:
return output
if self.artic_technician in [None, "None"]:
output['artic_technician'] = self.technician
else:
output['artic_technician'] = self.artic_technician
if report:
return output
output['gel_info'] = self.gel_info
output['gel_image_path'] = self.gel_image
output['dna_core_submission_number'] = self.dna_core_submission_number
@@ -2253,6 +2253,12 @@ class BasicSample(BaseClass):
@classmethod
def get_searchables(cls):
"""
Delivers a list of fields that can be used in fuzzy search.
Returns:
List[str]: List of fields.
"""
return [dict(label="Submitter ID", field="submitter_id")]
@classmethod
@@ -2381,22 +2387,14 @@ class WastewaterSample(BasicSample):
output_dict["submitter_id"] = output_dict['ww_full_sample_id']
return output_dict
def get_previous_ww_submission(self, current_artic_submission: WastewaterArtic):
try:
plates = [item['plate'] for item in current_artic_submission.source_plates]
except TypeError as e:
logger.error(f"source_plates must not be present")
plates = [item.rsl_plate_num for item in
self.submissions[:self.submissions.index(current_artic_submission)]]
subs = [sub for sub in self.submissions if sub.rsl_plate_num in plates]
# logger.debug(f"Submissions: {subs}")
try:
return subs[-1]
except IndexError:
return None
@classmethod
def get_searchables(cls):
def get_searchables(cls) -> List[str]:
"""
Delivers a list of fields that can be used in fuzzy search. Extends parent.
Returns:
List[str]: List of fields.
"""
searchables = super().get_searchables()
for item in ["ww_processing_num", "ww_full_sample_id", "rsl_number"]:
label = item.strip("ww_").replace("_", " ").replace("rsl", "RSL").title()