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Addition of Equipment and SubmissionType creation.

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This commit is contained in:
Landon Wark
2023-12-20 12:54:37 -06:00
parent 0dd51827a0
commit 0d64095e42
22 changed files with 755 additions and 123 deletions
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27
src/submissions/backend/excel/parser.py
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@@ -13,7 +13,7 @@ import logging, re
from collections import OrderedDict
from datetime import date
from dateutil.parser import parse, ParserError
from tools import check_not_nan, convert_nans_to_nones, Settings
from tools import check_not_nan, convert_nans_to_nones, Settings, is_missing
logger = logging.getLogger(f"submissions.{__name__}")
@@ -186,23 +186,15 @@ class InfoParser(object):
value = df.iat[relevant[item]['row']-1, relevant[item]['column']-1]
match item:
case "submission_type":
value, missing = is_missing(value)
value = value.title()
case _:
pass
value, missing = is_missing(value)
logger.debug(f"Setting {item} on {sheet} to {value}")
if check_not_nan(value):
if value != "None":
try:
dicto[item] = dict(value=value, missing=False)
except (KeyError, IndexError):
continue
else:
try:
dicto[item] = dict(value=value, missing=True)
except (KeyError, IndexError):
continue
else:
dicto[item] = dict(value=convert_nans_to_nones(value), missing=True)
try:
dicto[item] = dict(value=value, missing=missing)
except (KeyError, IndexError):
continue
return self.custom_parser(input_dict=dicto, xl=self.xl)
class ReagentParser(object):
@@ -293,7 +285,9 @@ class SampleParser(object):
self.xl = xl
self.submission_type = submission_type
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type)
logger.debug(f"sample_info_map: {sample_info_map}")
self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
logger.debug(f"plate_map: {self.plate_map}")
self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
if "plates" in sample_info_map:
self.plates = sample_info_map['plates']
@@ -332,10 +326,12 @@ class SampleParser(object):
Returns:
pd.DataFrame: Plate map grid
"""
logger.debug(f"Plate map location: {plate_map_location}")
df = self.xl.parse(plate_map_location['sheet'], header=None, dtype=object)
df = df.iloc[plate_map_location['start_row']-1:plate_map_location['end_row'], plate_map_location['start_column']-1:plate_map_location['end_column']]
df = pd.DataFrame(df.values[1:], columns=df.iloc[0])
df = df.set_index(df.columns[0])
logger.debug(f"Vanilla platemap: {df}")
# custom_mapper = get_polymorphic_subclass(models.BasicSubmission, self.submission_type)
custom_mapper = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
df = custom_mapper.custom_platemap(self.xl, df)
@@ -440,6 +436,7 @@ class SampleParser(object):
"""
result = None
new_samples = []
logger.debug(f"Starting samples: {pformat(self.samples)}")
for ii, sample in enumerate(self.samples):
# try:
# if sample['submitter_id'] in [check_sample['sample'].submitter_id for check_sample in new_samples]: