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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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15
src/submissions/backend/db/models/controls.py
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@@ -63,16 +63,16 @@ class ControlType(BaseClass):
Returns:
List[str]: list of subtypes available
"""
# Get first instance since all should have same subtypes
# Get mode of instance
# NOTE: Get first instance since all should have same subtypes
# NOTE: Get mode of instance
jsoner = getattr(self.instances[0], mode)
# logger.debug(f"JSON out: {jsoner.keys()}")
try:
# Pick genera (all should have same subtypes)
# NOTE: Pick genera (all should have same subtypes)
genera = list(jsoner.keys())[0]
except IndexError:
return []
# remove items that don't have relevant data
# NOTE: remove items that don't have relevant data
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
return subtypes
@@ -135,7 +135,6 @@ class Control(BaseClass):
"""
# logger.debug("loading json string into dict")
try:
# kraken = json.loads(self.kraken)
kraken = self.kraken
except TypeError:
kraken = {}
@@ -178,7 +177,7 @@ class Control(BaseClass):
data = self.__getattribute__(mode)
except TypeError:
data = {}
logger.debug(f"Length of data: {len(data)}")
# logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:
_dict = dict(
@@ -236,7 +235,7 @@ class Control(BaseClass):
models.Control|List[models.Control]: Control object of interest.
"""
query: Query = cls.__database_session__.query(cls)
# by control type
# NOTE: by control type
match control_type:
case ControlType():
# logger.debug(f"Looking up control by control type: {control_type}")
@@ -246,7 +245,7 @@ class Control(BaseClass):
query = query.join(ControlType).filter(ControlType.name == control_type)
case _:
pass
# by date range
# NOTE: by date range
if start_date is not None and end_date is None:
logger.warning(f"Start date with no end date, using today.")
end_date = date.today()