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Updated parsers and chart constructors.

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This commit is contained in:
Landon Wark
2023-04-27 12:51:53 -05:00
parent 8a0a9aa69c
commit dff5a5aa1e
9 changed files with 59 additions and 19 deletions
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14
src/submissions/backend/excel/parser.py
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@@ -107,8 +107,8 @@ class SheetParser(object):
"""
for ii, row in df.iterrows():
# skip positive control
if ii == 11:
continue
# if ii == 12:
# continue
logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
if not isinstance(row[2], float) and check_not_nan(row[1]):
# must be prefixed with 'lot_' to be recognized by gui
@@ -117,7 +117,10 @@ class SheetParser(object):
except AttributeError:
pass
if reagent_type == "//":
reagent_type = row[0].replace(' ', '_').lower().strip()
if check_not_nan(row[2]):
reagent_type = row[0].replace(' ', '_').lower().strip()
else:
continue
try:
output_var = row[2].upper()
except AttributeError:
@@ -142,10 +145,11 @@ class SheetParser(object):
# reagents
# must be prefixed with 'lot_' to be recognized by gui
# Todo: find a more adaptable way to read reagents.
reagent_range = submission_info.iloc[1:13, 4:8]
reagent_range = submission_info.iloc[1:14, 4:8]
logger.debug(reagent_range)
parse_reagents(reagent_range)
# get individual sample info
sample_parser = SampleParser(submission_info.iloc[15:111])
sample_parser = SampleParser(submission_info.iloc[16:112])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
logger.debug(f"Parser result: {self.sub}")
self.sub['samples'] = sample_parse()