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Autofill excel sheet

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This commit is contained in:
Landon Wark
2023-07-21 13:55:15 -05:00
parent ba35696055
commit f6e270f52d
10 changed files with 189 additions and 67 deletions
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25
src/submissions/backend/excel/parser.py
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@@ -38,7 +38,7 @@ class SheetParser(object):
self.filepath = filepath
# Open excel file
try:
self.xl = pd.ExcelFile(filepath.__str__())
self.xl = pd.ExcelFile(filepath)
except ValueError as e:
logger.error(f"Incorrect value: {e}")
self.xl = None
@@ -95,7 +95,7 @@ class SheetParser(object):
submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
if check_not_nan(submission_info.iloc[10][1]):
self.sub['rsl_plate_num'] = RSLNamer(submission_info.iloc[10][1]).parsed_name
self.sub['rsl_plate_num'] = RSLNamer(ctx=self.ctx, instr=submission_info.iloc[10][1]).parsed_name
else:
# self.sub['rsl_plate_num'] = RSLNamer(self.filepath).parsed_name
self.sub['rsl_plate_num'] = None
@@ -103,6 +103,10 @@ class SheetParser(object):
self.sub['submitting_lab'] = submission_info.iloc[0][3]
self.sub['sample_count'] = submission_info.iloc[2][3]
self.sub['extraction_kit'] = submission_info.iloc[3][3]
if check_not_nan(submission_info.iloc[1][3]):
self.sub['submission_type'] = dict(value=submission_info.iloc[1][3], parsed=True)
else:
self.sub['submission_type'] = dict(value=self.sub['submission_type'], parsed=False)
return submission_info
def parse_bacterial_culture(self) -> None:
@@ -170,7 +174,7 @@ class SheetParser(object):
parse_reagents(reagent_range)
# get individual sample info
sample_parser = SampleParser(self.ctx, submission_info.iloc[16:112])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type']['value'].replace(' ', '_').lower()}_samples")
logger.debug(f"Parser result: {self.sub}")
self.sample_result, self.sub['samples'] = sample_parse()
@@ -234,14 +238,18 @@ class SheetParser(object):
# set qpcr reagent range
pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
# compile technician info from all sheets
self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
if all(map(check_not_nan, [enrichment_info.columns[2], extraction_info.columns[2], qprc_info.columns[2]])):
parsed = True
else:
parsed = False
self.sub['technician'] = dict(value=f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}", parsed=parsed)
self.sub['reagents'] = []
parse_reagents(enr_reagent_range)
parse_reagents(ext_reagent_range)
parse_reagents(pcr_reagent_range)
# parse samples
sample_parser = SampleParser(self.ctx, submission_info.iloc[16:], elution_map=retrieve_elution_map())
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type']['value'].lower()}_samples")
self.sample_result, self.sub['samples'] = sample_parse()
self.sub['csv'] = self.xl.parse("Copy to import file", dtype=object)
@@ -249,6 +257,7 @@ class SheetParser(object):
"""
pulls info specific to wastewater_arctic submission type
"""
self.sub['submission_type'] = dict(value=self.sub['submission_type'], parsed=True)
def parse_reagents(df:pd.DataFrame):
logger.debug(df)
for ii, row in df.iterrows():
@@ -306,7 +315,7 @@ class SheetParser(object):
sub_reagent_range = submission_info.iloc[56:, 1:4].dropna(how='all')
biomek_reagent_range = biomek_info.iloc[60:, 0:3].dropna(how='all')
self.sub['submitter_plate_num'] = ""
self.sub['rsl_plate_num'] = RSLNamer(self.filepath.__str__()).parsed_name
self.sub['rsl_plate_num'] = RSLNamer(ctx=self.ctx, instr=self.filepath.__str__()).parsed_name
self.sub['submitted_date'] = biomek_info.iloc[1][1]
self.sub['submitting_lab'] = "Enterics Wastewater Genomics"
self.sub['sample_count'] = submission_info.iloc[4][6]
@@ -317,7 +326,7 @@ class SheetParser(object):
parse_reagents(biomek_reagent_range)
samples = massage_samples(biomek_info.iloc[22:31, 0:])
sample_parser = SampleParser(self.ctx, pd.DataFrame.from_records(samples))
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type']['value'].lower()}_samples")
self.sample_result, self.sub['samples'] = sample_parse()
def to_pydantic(self) -> PydSubmission:
@@ -497,7 +506,7 @@ class PCRParser(object):
return
# self.pcr = OrderedDict()
self.pcr = {}
namer = RSLNamer(filepath.__str__())
namer = RSLNamer(ctx=self.ctx, instr=filepath.__str__())
self.plate_num = namer.parsed_name
self.submission_type = namer.submission_type
logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")