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Conversion of some functions to generators.

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This commit is contained in:
lwark
2024-07-31 13:08:56 -05:00
parent eb6cdc63e2
commit 8266275354
15 changed files with 374 additions and 369 deletions
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32
src/submissions/backend/excel/parser.py
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@@ -84,8 +84,9 @@ class SheetParser(object):
if extraction_kit is None:
extraction_kit = self.sub['extraction_kit']
# logger.debug(f"Parsing reagents for {extraction_kit}")
self.sub['reagents'] = ReagentParser(xl=self.xl, submission_type=self.submission_type,
extraction_kit=extraction_kit).parse_reagents()
parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
extraction_kit=extraction_kit)
self.sub['reagents'] = [item for item in parser.parse_reagents()]
def parse_samples(self):
"""
@@ -303,21 +304,21 @@ class ReagentParser(object):
if isinstance(submission_type, dict):
submission_type = submission_type['value']
reagent_map = self.kit_object.construct_xl_map_for_use(submission_type)
reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
try:
del reagent_map['info']
except KeyError:
pass
return reagent_map
def parse_reagents(self) -> List[dict]:
def parse_reagents(self) -> Generator[dict, None, None]:
"""
Extracts reagent information from the excel form.
Extracts reagent information from the Excel form.
Returns:
List[PydReagent]: List of parsed reagents.
"""
listo = []
# 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']}
@@ -337,9 +338,8 @@ class ReagentParser(object):
else:
comment = ""
except (KeyError, IndexError):
listo.append(
dict(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True))
continue
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
@@ -355,9 +355,9 @@ class ReagentParser(object):
logger.warning(f"name is not a string.")
check = True
if check:
listo.append(dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
missing=missing))
return listo
yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
missing=missing)
# return listo
class SampleParser(object):
@@ -556,14 +556,14 @@ class EquipmentParser(object):
self.xl = xl
self.map = self.fetch_equipment_map()
def fetch_equipment_map(self) -> List[dict]:
def fetch_equipment_map(self) -> dict:
"""
Gets the map of equipment locations in the submission type's spreadsheet
Returns:
List[dict]: List of locations
"""
return self.submission_type.construct_equipment_map()
return {k: v for k, v in self.submission_type.construct_equipment_map()}
def get_asset_number(self, input: str) -> str:
"""
@@ -642,14 +642,14 @@ class TipParser(object):
self.xl = xl
self.map = self.fetch_tip_map()
def fetch_tip_map(self) -> List[dict]:
def fetch_tip_map(self) -> dict:
"""
Gets the map of equipment locations in the submission type's spreadsheet
Returns:
List[dict]: List of locations
"""
return self.submission_type.construct_tips_map()
return {k:v for k,v in self.submission_type.construct_tips_map()}
def parse_tips(self) -> List[dict]:
"""