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Second round of code cleanup.

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This commit is contained in:
lwark
2024-10-30 07:34:39 -05:00
parent 1f83b61c81
commit ba1b3e5cf3
19 changed files with 176 additions and 110 deletions
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36
src/submissions/backend/excel/parser.py
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@@ -2,6 +2,7 @@
contains parser objects for pulling values from client generated submission sheets.
'''
import json
import sys
from copy import copy
from getpass import getuser
from pprint import pformat
@@ -95,6 +96,7 @@ class SheetParser(object):
parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
extraction_kit=extraction_kit)
self.sub['reagents'] = parser.parse_reagents()
logger.debug(f"Reagents out of parser: {pformat(self.sub['reagents'])}")
def parse_samples(self):
"""
@@ -273,7 +275,8 @@ class ReagentParser(object):
# logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl
def fetch_kit_info_map(self, submission_type: str) -> dict:
@report_result
def fetch_kit_info_map(self, submission_type: str) -> Tuple[Report, dict]:
"""
Gets location of kit reagents from database
@@ -283,7 +286,7 @@ class ReagentParser(object):
Returns:
dict: locations of reagent info for the kit.
"""
report = Report()
if isinstance(submission_type, dict):
submission_type = submission_type['value']
reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
@@ -291,7 +294,12 @@ class ReagentParser(object):
del reagent_map['info']
except KeyError:
pass
return reagent_map
# logger.debug(f"Reagent map: {pformat(reagent_map)}")
if not reagent_map.keys():
report.add_result(Result(owner=__name__, code=0, msg=f"No kit map found for {self.kit_object.name}.\n\n"
f"Are you sure you used the right kit?",
status="Critical"))
return report, reagent_map
def parse_reagents(self) -> Generator[dict, None, None]:
"""
@@ -401,6 +409,7 @@ class SampleParser(object):
"""
invalids = [0, "0", "EMPTY"]
smap = self.sample_info_map['plate_map']
print(smap)
ws = self.xl[smap['sheet']]
plate_map_samples = []
for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1):
@@ -469,8 +478,10 @@ class SampleParser(object):
yield new
else:
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])
# 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])
plate_map_samples = sorted(copy(self.plate_map_samples), key=itemgetter('id'))
lookup_samples = sorted(copy(self.lookup_samples), key=itemgetter(merge_on_id))
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:
@@ -483,6 +494,8 @@ class SampleParser(object):
lookup_samples[ii] = {}
else:
logger.warning(f"Match for {psample['id']} not direct, running search.")
searchables = [(jj, sample) for jj, sample in enumerate(lookup_samples)
if merge_on_id in sample.keys()]
# for jj, lsample in enumerate(lookup_samples):
# try:
# check = lsample[merge_on_id] == psample['id']
@@ -494,14 +507,18 @@ class SampleParser(object):
# break
# else:
# new = psample
jj, new = next(((jj, lsample) for jj, lsample in enumerate(lookup_samples) if lsample[merge_on_id] == psample['id']), (-1, psample))
jj, new = next(((jj, lsample | psample) for jj, lsample in searchables
if lsample[merge_on_id] == psample['id']), (-1, psample))
logger.debug(f"Assigning from index {jj} - {new}")
if jj >= 0:
lookup_samples[jj] = {}
if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
new['submitter_id'] = psample['id']
new = self.sub_object.parse_samples(new)
del new['id']
try:
del new['id']
except KeyError:
pass
yield new
@@ -586,7 +603,7 @@ class EquipmentParser(object):
nickname=eq.nickname)
except AttributeError:
logger.error(f"Unable to add {eq} to list.")
class TipParser(object):
"""
@@ -649,7 +666,7 @@ class TipParser(object):
yield dict(name=eq.name, role=k, lot=lot)
except AttributeError:
logger.error(f"Unable to add {eq} to PydTips list.")
class PCRParser(object):
"""Object to pull data from Design and Analysis PCR export file."""
@@ -705,4 +722,3 @@ class PCRParser(object):
pcr['imported_by'] = getuser()
# logger.debug(f"PCR: {pformat(pcr)}")
return pcr