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

Code cleanup, dependency update, various bug fixes

Browse Source
This commit is contained in:
lwark
2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
Download Patch File Download Diff File Expand all files Collapse all files

77
src/submissions/backend/excel/parser.py
View File

@@ -543,7 +543,6 @@ class EquipmentParser(object):
def __init__(self, xl: Workbook, submission_type: str|SubmissionType) -> None:
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
self.map = self.fetch_equipment_map()
@@ -555,7 +554,6 @@ class EquipmentParser(object):
Returns:
List[dict]: List of locations
"""
# submission_type = SubmissionType.query(name=self.submission_type)
return self.submission_type.construct_equipment_map()
def get_asset_number(self, input: str) -> str:
@@ -569,7 +567,7 @@ class EquipmentParser(object):
str: asset number
"""
regex = Equipment.get_regex()
logger.debug(f"Using equipment regex: {regex} on {input}")
# logger.debug(f"Using equipment regex: {regex} on {input}")
try:
return regex.search(input).group().strip("-")
except AttributeError:
@@ -582,11 +580,10 @@ class EquipmentParser(object):
Returns:
List[PydEquipment]: list of equipment
"""
logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
# logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
output = []
# logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames:
# df = self.xl.parse(sheet, header=None, dtype=object)
ws = self.xl[sheet]
try:
relevant = [item for item in self.map if item['sheet'] == sheet]
@@ -595,7 +592,6 @@ class EquipmentParser(object):
# logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = ""
for equipment in relevant:
# asset = df.iat[equipment['name']['row']-1, equipment['name']['column']-1]
asset = ws.cell(equipment['name']['row'], equipment['name']['column'])
if not check_not_nan(asset):
asset = previous_asset
@@ -603,7 +599,6 @@ class EquipmentParser(object):
previous_asset = asset
asset = self.get_asset_number(input=asset)
eq = Equipment.query(asset_number=asset)
# process = df.iat[equipment['process']['row']-1, equipment['process']['column']-1]
process = ws.cell(row=equipment['process']['row'], column=equipment['process']['column'])
try:
output.append(
@@ -614,72 +609,6 @@ class EquipmentParser(object):
# logger.debug(f"Here is the output so far: {pformat(output)}")
return output
# class PCRParser(object):
# """
# Object to pull data from Design and Analysis PCR export file.
# """
#
# def __init__(self, filepath: Path | None = None) -> None:
# """
# Initializes object.
#
# Args:
# filepath (Path | None, optional): file to parse. Defaults to None.
# """
# logger.debug(f"Parsing {filepath.__str__()}")
# if filepath == None:
# logger.error(f"No filepath given.")
# self.xl = None
# else:
# try:
# self.xl = pd.ExcelFile(filepath.__str__())
# except ValueError as e:
# logger.error(f"Incorrect value: {e}")
# self.xl = None
# except PermissionError:
# logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
# return
# self.parse_general(sheet_name="Results")
# namer = RSLNamer(filename=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}")
# parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
# self.samples = parser.parse_pcr(xl=self.xl, rsl_number=self.plate_num)
#
# def parse_general(self, sheet_name: str):
# """
# Parse general info rows for all types of PCR results
#
# Args:
# sheet_name (str): Name of sheet in excel workbook that holds info.
# """
# self.pcr = {}
# df = self.xl.parse(sheet_name=sheet_name, dtype=object).fillna("")
# self.pcr['comment'] = df.iloc[0][1]
# self.pcr['operator'] = df.iloc[1][1]
# self.pcr['barcode'] = df.iloc[2][1]
# self.pcr['instrument'] = df.iloc[3][1]
# self.pcr['block_type'] = df.iloc[4][1]
# self.pcr['instrument_name'] = df.iloc[5][1]
# self.pcr['instrument_serial'] = df.iloc[6][1]
# self.pcr['heated_cover_serial'] = df.iloc[7][1]
# self.pcr['block_serial'] = df.iloc[8][1]
# self.pcr['run-start'] = df.iloc[9][1]
# self.pcr['run_end'] = df.iloc[10][1]
# self.pcr['run_duration'] = df.iloc[11][1]
# self.pcr['sample_volume'] = df.iloc[12][1]
# self.pcr['cover_temp'] = df.iloc[13][1]
# self.pcr['passive_ref'] = df.iloc[14][1]
# self.pcr['pcr_step'] = df.iloc[15][1]
# self.pcr['quant_cycle_method'] = df.iloc[16][1]
# self.pcr['analysis_time'] = df.iloc[17][1]
# self.pcr['software'] = df.iloc[18][1]
# self.pcr['plugin'] = df.iloc[19][1]
# self.pcr['exported_on'] = df.iloc[20][1]
# self.pcr['imported_by'] = getuser()
class PCRParser(object):
"""Object to pull data from Design and Analysis PCR export file."""
@@ -690,7 +619,7 @@ class PCRParser(object):
Args:
filepath (Path | None, optional): file to parse. Defaults to None.
"""
logger.debug(f'Parsing {filepath.__str__()}')
# logger.debug(f'Parsing {filepath.__str__()}')
if filepath is None:
logger.error('No filepath given.')
self.xl = None