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Increasing generator usage.

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This commit is contained in:
lwark
2024-10-08 14:55:54 -05:00
parent eaf6c156b3
commit ae5fb1b48f
9 changed files with 81 additions and 151 deletions
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13
src/submissions/backend/db/models/kits.py
View File

@@ -142,8 +142,8 @@ class KitType(BaseClass):
"""
return f"<KitType({self.name})>"
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> List[
ReagentRole]:
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> Generator[
ReagentRole, None, None]:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
@@ -168,9 +168,9 @@ class KitType(BaseClass):
relevant_associations = [item for item in self.kit_reagentrole_associations]
if required:
# logger.debug(f"Filtering by required.")
return [item.reagent_role for item in relevant_associations if item.required == 1]
return (item.reagent_role for item in relevant_associations if item.required == 1)
else:
return [item.reagent_role for item in relevant_associations]
return (item.reagent_role for item in relevant_associations)
# TODO: Move to BasicSubmission?
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str)]:
@@ -198,6 +198,7 @@ class KitType(BaseClass):
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
for assoc in assocs:
try:
logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
yield assoc.reagent_role.name, assoc.uses
except TypeError:
continue
@@ -764,14 +765,14 @@ class SubmissionType(BaseClass):
tmap = {}
yield item.tip_role.name, tmap
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
def get_equipment(self, extraction_kit: str | KitType | None = None) -> Generator['PydEquipmentRole', None, None]:
"""
Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns:
List[PydEquipmentRole]: List of equipment roles
"""
return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment)
def get_processes_for_role(self, equipment_role: str | EquipmentRole, kit: str | KitType | None = None) -> list:
"""

11
src/submissions/backend/db/models/submissions.py
View File

@@ -219,11 +219,11 @@ class BasicSubmission(BaseClass):
if len(args) == 1:
try:
return output[args[0]]
except KeyError:
except KeyError as e:
if "pytest" in sys.modules and args[0] == "abbreviation":
return "BS"
else:
raise KeyError("args[0]")
raise KeyError(f"{args[0]} not found in {output}")
return output
@classmethod
@@ -237,6 +237,13 @@ class BasicSubmission(BaseClass):
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
"""
logger.debug(f"Running search for {sub_type}")
if isinstance(sub_type, dict):
try:
sub_type = sub_type['value']
except KeyError as e:
logger.error(f"Couldn't extract value from {sub_type}")
raise e
match sub_type:
case str():
return SubmissionType.query(name=sub_type)

82
src/submissions/backend/excel/parser.py
View File

@@ -80,14 +80,6 @@ class SheetParser(object):
self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
self.parse_info()
[self.sub.__setitem__(k, v) for k, v in info.items()]
# for k, v in info.items():
# match k:
# # NOTE: exclude samples.
# case "sample":
# logger.debug(f"Sample found: {k}: {v}")
# continue
# case _:
# self.sub[k] = v
def parse_reagents(self, extraction_kit: str | None = None):
"""
@@ -147,30 +139,8 @@ class SheetParser(object):
Returns:
PydSubmission: output pydantic model
"""
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
# pyd_dict = copy(self.sub)
# self.sub['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
# logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
# self.sub['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
# logger.debug(f"Equipment: {self.sub['equipment']}")
# try:
# check = bool(self.sub['equipment'])
# except TypeError:
# check = False
# if check:
# self.sub['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
# else:
# self.sub['equipment'] = None
# try:
# check = bool(self.sub['tips'])
# except TypeError:
# check = False
# if check:
# self.sub['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
# else:
# self.sub['tips'] = None
return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
# return psm
class InfoParser(object):
@@ -298,6 +268,7 @@ class ReagentParser(object):
if isinstance(extraction_kit, dict):
extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit)
# logger.debug(f"Got extraction kit object: {self.kit_object}")
self.map = self.fetch_kit_info_map(submission_type=submission_type)
# logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl
@@ -329,15 +300,14 @@ class ReagentParser(object):
Returns:
List[PydReagent]: List of parsed reagents.
"""
# listo = []
for sheet in self.xl.sheetnames:
ws = self.xl[sheet]
relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}:
continue
for item in relevant:
# logger.debug(f"Attempting to scrape: {item}")
logger.debug(f"Attempting to scrape: {item}")
try:
reagent = relevant[item]
name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
@@ -350,16 +320,15 @@ class ReagentParser(object):
comment = ""
except (KeyError, IndexError):
yield dict(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True)
# continue
# NOTE: If the cell is blank tell the PydReagent
if check_not_nan(lot):
missing = False
else:
missing = True
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot)
# logger.debug(
# f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
logger.debug(
f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
try:
check = name.lower() != "not applicable"
except AttributeError:
@@ -368,7 +337,6 @@ class ReagentParser(object):
if check:
yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
missing=missing)
# return listo
class SampleParser(object):
@@ -480,34 +448,6 @@ class SampleParser(object):
lookup_samples.append(self.samp_object.parse_sample(row_dict))
return lookup_samples
# def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
# """
# Parse merged platemap/lookup info into dicts/samples
#
# Returns:
# List[dict]|List[models.BasicSample]: List of samples
# """
# result = None
# new_samples = []
# # logger.debug(f"Starting samples: {pformat(self.samples)}")
# for sample in self.samples:
# translated_dict = {}
# for k, v in sample.items():
# match v:
# case dict():
# v = None
# case float():
# v = convert_nans_to_nones(v)
# case _:
# v = v
# translated_dict[k] = convert_nans_to_nones(v)
# translated_dict['sample_type'] = f"{self.submission_type} Sample"
# translated_dict = self.sub_object.parse_samples(translated_dict)
# translated_dict = self.samp_object.parse_sample(translated_dict)
# # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
# new_samples.append(PydSample(**translated_dict))
# return result, new_samples
def parse_samples(self) -> Generator[dict, None, None]:
"""
Merges sample info from lookup table and plate map.
@@ -522,9 +462,8 @@ class SampleParser(object):
merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
# print(pformat(plate_map_samples))
# print(pformat(lookup_samples))
for ii, psample in enumerate(plate_map_samples):
# NOTE: See if we can do this the easy way and just use the same list index.
try:
check = psample['id'] == lookup_samples[ii][merge_on_id]
except (KeyError, IndexError):
@@ -534,7 +473,7 @@ class SampleParser(object):
new = lookup_samples[ii] | psample
lookup_samples[ii] = {}
else:
# logger.warning(f"Match for {psample['id']} not direct, running search.")
logger.warning(f"Match for {psample['id']} not direct, running search.")
for jj, lsample in enumerate(lookup_samples):
try:
check = lsample[merge_on_id] == psample['id']
@@ -551,9 +490,6 @@ class SampleParser(object):
new = self.sub_object.parse_samples(new)
del new['id']
yield new
# samples.append(new)
# samples = remove_key_from_list_of_dicts(samples, "id")
# return sorted(samples, key=lambda k: (k['row'], k['column']))
class EquipmentParser(object):