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Added in ability to overwrite submissions.

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This commit is contained in:
Landon Wark
2023-01-26 14:54:32 -06:00
parent 3c308f6559
commit bbb65d3fe6
9 changed files with 151 additions and 93 deletions
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82
src/submissions/backend/excel/parser.py
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@@ -45,13 +45,14 @@ class SheetParser(object):
def _parse_generic(self, sheet_name:str):
submission_info = self.xl.parse(sheet_name=sheet_name)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
self.sub['rsl_plate_num'] = str(submission_info.iloc[10][1])
self.sub['submitted_date'] = submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
self.sub['submitting_lab'] = submission_info.iloc[0][3]
self.sub['sample_count'] = str(submission_info.iloc[2][3])
self.sub['extraction_kit'] = submission_info.iloc[3][3]
submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1] #if pd.isnull(submission_info.iloc[0][1]) else string_formatter(submission_info.iloc[0][1])
self.sub['rsl_plate_num'] = submission_info.iloc[10][1] #if pd.isnull(submission_info.iloc[10][1]) else string_formatter(submission_info.iloc[10][1])
self.sub['submitted_date'] = submission_info.iloc[1][1] #if pd.isnull(submission_info.iloc[1][1]) else submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
self.sub['submitting_lab'] = submission_info.iloc[0][3] #if pd.isnull(submission_info.iloc[0][3]) else string_formatter(submission_info.iloc[0][3])
self.sub['sample_count'] = submission_info.iloc[2][3] #if pd.isnull(submission_info.iloc[2][3]) else string_formatter(submission_info.iloc[2][3])
self.sub['extraction_kit'] = submission_info.iloc[3][3] #if #pd.isnull(submission_info.iloc[3][3]) else string_formatter(submission_info.iloc[3][3])
return submission_info
@@ -67,16 +68,17 @@ class SheetParser(object):
tech = ", ".join(tech_reg.findall(tech))
self.sub['technician'] = tech
# reagents
self.sub['lot_wash_1'] = submission_info.iloc[1][6]
self.sub['lot_wash_2'] = submission_info.iloc[2][6]
self.sub['lot_binding_buffer'] = submission_info.iloc[3][6]
self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6]
self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6]
self.sub['lot_elution_buffer'] = submission_info.iloc[6][6]
self.sub['lot_isopropanol'] = submission_info.iloc[9][6]
self.sub['lot_ethanol'] = submission_info.iloc[10][6]
self.sub['lot_positive_control'] = submission_info.iloc[103][1]
self.sub['lot_plate'] = submission_info.iloc[12][6]
self.sub['lot_wash_1'] = submission_info.iloc[1][6] #if pd.isnull(submission_info.iloc[1][6]) else string_formatter(submission_info.iloc[1][6])
self.sub['lot_wash_2'] = submission_info.iloc[2][6] #if pd.isnull(submission_info.iloc[2][6]) else string_formatter(submission_info.iloc[2][6])
self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] #if pd.isnull(submission_info.iloc[3][6]) else string_formatter(submission_info.iloc[3][6])
self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] #if pd.isnull(submission_info.iloc[4][6]) else string_formatter(submission_info.iloc[4][6])
self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] #if np.nan(submission_info.iloc[5][6]) else string_formatter(submission_info.iloc[5][6])
self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] #if pd.isnull(submission_info.iloc[6][6]) else string_formatter(submission_info.iloc[6][6])
self.sub['lot_isopropanol'] = submission_info.iloc[9][6] #if pd.isnull(submission_info.iloc[9][6]) else string_formatter(submission_info.iloc[9][6])
self.sub['lot_ethanol'] = submission_info.iloc[10][6] #if pd.isnull(submission_info.iloc[10][6]) else string_formatter(submission_info.iloc[10][6])
self.sub['lot_positive_control'] = submission_info.iloc[103][1] #if pd.isnull(submission_info.iloc[103][1]) else string_formatter(submission_info.iloc[103][1])
self.sub['lot_plate'] = submission_info.iloc[12][6] #if pd.isnull(submission_info.iloc[12][6]) else string_formatter(submission_info.iloc[12][6])
sample_parser = SampleParser(submission_info.iloc[15:111])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
logger.debug(f"Parser result: {self.sub}")
@@ -86,25 +88,26 @@ class SheetParser(object):
def _parse_wastewater(self):
# submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
enrichment_info = self.xl.parse("Enrichment Worksheet")
extraction_info = self.xl.parse("Extraction Worksheet")
qprc_info = self.xl.parse("qPCR Worksheet")
enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
extraction_info = self.xl.parse("Extraction Worksheet", dtype=object)
qprc_info = self.xl.parse("qPCR Worksheet", dtype=object)
self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
# reagents
self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14]
self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14]
self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14]
self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14]
self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14]
self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14]
self.sub['lot_wash'] = extraction_info.iloc[2][14]
self.sub['lot_ethanol'] = extraction_info.iloc[3][14]
self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14]
self.sub['lot_master_mix'] = qprc_info.iloc[0][14]
self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14]
self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14]
self.sub['lot_positive_control'] = qprc_info.iloc[3][14]
self.sub['lot_ddh2o'] = qprc_info.iloc[4][14]
logger.debug(qprc_info)
self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] #if pd.isnull(enrichment_info.iloc[0][14]) else string_formatter(enrichment_info.iloc[0][14])
self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] #if pd.isnull(enrichment_info.iloc[1][14]) else string_formatter(enrichment_info.iloc[1][14])
self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] #if pd.isnull(enrichment_info.iloc[2][14]) else string_formatter(enrichment_info.iloc[2][14])
self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] #if pd.isnull(enrichment_info.iloc[3][14]) else string_formatter(enrichment_info.iloc[3][14])
self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] #if pd.isnull(extraction_info.iloc[0][14]) else string_formatter(extraction_info.iloc[0][14])
self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] #if pd.isnull(extraction_info.iloc[1][14]) else string_formatter(extraction_info.iloc[1][14])
self.sub['lot_wash'] = extraction_info.iloc[2][14] #if pd.isnull(extraction_info.iloc[2][14]) else string_formatter(extraction_info.iloc[2][14])
self.sub['lot_ethanol'] = extraction_info.iloc[3][14] #if pd.isnull(extraction_info.iloc[3][14]) else string_formatter(extraction_info.iloc[3][14])
self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] #if pd.isnull(extraction_info.iloc[4][14]) else string_formatter(extraction_info.iloc[4][14])
self.sub['lot_master_mix'] = qprc_info.iloc[0][14] #if pd.isnull(qprc_info.iloc[0][14]) else string_formatter(qprc_info.iloc[0][14])
self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] #if pd.isnull(qprc_info.iloc[1][14]) else string_formatter(qprc_info.iloc[1][14])
self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
sample_parser = SampleParser(submission_info.iloc[16:40])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
self.sub['samples'] = sample_parse()
@@ -164,4 +167,13 @@ class SampleParser(object):
new.well_number = sample['Unnamed: 1']
new_list.append(new)
return new_list
def string_formatter(input):
logger.debug(f"{input} : {type(input)}")
match input:
case int() | float() | np.float64:
return "{:0.0f}".format(input)
case _:
return input