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Last minute save of new pcr parser.

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This commit is contained in:
lwark
2024-05-16 15:32:58 -05:00
parent bbcbd35127
commit d1bf12e8d1
3 changed files with 199 additions and 103 deletions
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32
src/submissions/backend/db/models/kits.py
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@@ -156,11 +156,11 @@ class KitType(BaseClass):
# logger.debug(f"Constructing xl map with str {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if
item.submission_type.name == submission_type]
st_assoc = [item for item in self.used_for if submission_type == item.name][0]
# st_assoc = [item for item in self.used_for if submission_type == item.name][0]
case SubmissionType():
# logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if item.submission_type == submission_type]
st_assoc = submission_type
# st_assoc = submission_type
case _:
raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
@@ -279,9 +279,9 @@ class ReagentType(BaseClass):
ReagentType|List[ReagentType]: ReagentType or list of ReagentTypes matching filter.
"""
query: Query = cls.__database_session__.query(cls)
if (kit_type != None and reagent == None) or (reagent != None and kit_type == None):
if (kit_type is not None and reagent is None) or (reagent is not None and kit_type is None):
raise ValueError("Cannot filter without both reagent and kit type.")
elif kit_type == None and reagent == None:
elif kit_type is None and reagent is None:
pass
else:
match kit_type:
@@ -296,7 +296,7 @@ class ReagentType(BaseClass):
reagent = Reagent.query(lot_number=reagent)
case _:
pass
assert reagent.type != []
assert reagent.type
# logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
# logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
result = list(set(kit_type.reagent_types).intersection(reagent.type))
@@ -353,7 +353,7 @@ class Reagent(BaseClass):
"submission") #: Association proxy to SubmissionSampleAssociation.samples
def __repr__(self):
if self.name != None:
if self.name is not None:
return f"<Reagent({self.name}-{self.lot})>"
else:
return f"<Reagent({self.type.name}-{self.lot})>"
@@ -368,7 +368,7 @@ class Reagent(BaseClass):
Returns:
dict: representation of the reagent's attributes
"""
if extraction_kit != None:
if extraction_kit is not None:
# Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try:
reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
@@ -412,10 +412,10 @@ class Reagent(BaseClass):
report = Report()
logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})")
rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
if rt != None:
if rt is not None:
logger.debug(f"got reagenttype {rt}")
assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
if assoc != None:
if assoc is not None:
if assoc.last_used != self.lot:
logger.debug(f"Updating {assoc} last used to {self.lot}")
assoc.last_used = self.lot
@@ -658,14 +658,10 @@ class SubmissionType(BaseClass):
output = {}
# logger.debug("Iterating through equipment roles")
for item in self.submissiontype_equipmentrole_associations:
map = item.uses
if map is None:
map = {}
# try:
output[item.equipment_role.name] = map
# except TypeError:
# pass
# output.append(map)
emap = item.uses
if emap is None:
emap = {}
output[item.equipment_role.name] = emap
return output
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
@@ -737,7 +733,7 @@ class SubmissionType(BaseClass):
match key:
case str():
# logger.debug(f"Looking up submission type by info-map key str: {key}")
query = query.filter(cls.info_map.op('->')(key) != None)
query = query.filter(cls.info_map.op('->')(key) is not None)
case _:
pass
return cls.execute_query(query=query, limit=limit)