landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

controls working

Browse Source
This commit is contained in:
Landon Wark
2023-01-23 14:28:24 -06:00
parent d17ee5862d
commit 7a53cfd9a1
9 changed files with 625 additions and 159 deletions
Download Patch File Download Diff File Expand all files Collapse all files

30
src/submissions/backend/excel/parser.py
View File

@@ -54,7 +54,6 @@ class SheetParser(object):
def _parse_bacterial_culture(self):
# submission_info = self.xl.parse("Sample List")
submission_info = self._parse_generic("Sample List")
# iloc is [row][column] and the first row is set as header row so -2
tech = str(submission_info.iloc[11][1])
@@ -86,13 +85,6 @@ class SheetParser(object):
enrichment_info = self.xl.parse("Enrichment Worksheet")
extraction_info = self.xl.parse("Extraction Worksheet")
qprc_info = self.xl.parse("qPCR Worksheet")
# iloc is [row][column] and the first row is set as header row so -2
# 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]
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]
@@ -112,24 +104,6 @@ class SheetParser(object):
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()
# tech = str(submission_info.iloc[11][1])
# if tech == "nan":
# tech = "Unknown"
# elif len(tech.split(",")) > 1:
# tech_reg = re.compile(r"[A-Z]{2}")
# tech = ", ".join(tech_reg.findall(tech))
# 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'] = None #submission_info.iloc[103][1]
# self.sub['lot_plate'] = submission_info.iloc[12][6]
class SampleParser(object):
@@ -147,9 +121,9 @@ class SampleParser(object):
new.sample_id = sample['Unnamed: 1']
new.organism = sample['Unnamed: 2']
new.concentration = sample['Unnamed: 3']
print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
# print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
try:
not_a_nan = not np.isnan(new.sample_id)
not_a_nan = not np.isnan(new.sample_id) and new.sample_id.lower() != 'blank'
except TypeError:
not_a_nan = True
if not_a_nan: