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Update to autofill.

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This commit is contained in:
Landon Wark
2023-09-20 09:19:59 -05:00
parent 0c843d1561
commit 82ab06efad
13 changed files with 378 additions and 149 deletions
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68
src/submissions/backend/excel/parser.py
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@@ -14,7 +14,7 @@ import re
import numpy as np
from datetime import date
from dateutil.parser import parse, ParserError
from tools import check_not_nan, RSLNamer, convert_nans_to_nones, Settings
from tools import check_not_nan, RSLNamer, convert_nans_to_nones, Settings, convert_well_to_row_column
from frontend.custom_widgets.pop_ups import SubmissionTypeSelector, KitSelector
logger = logging.getLogger(f"submissions.{__name__}")
@@ -48,14 +48,12 @@ class SheetParser(object):
# make decision about type of sample we have
self.sub['submission_type'] = self.type_decider()
# # grab the info map from the submission type in database
# self.info_map = self.fetch_kit_info_map()
self.parse_info()
self.import_kit_validation_check()
self.parse_reagents()
self.import_reagent_validation_check()
self.parse_samples()
# self.sub['sample_count'] = len(self.sub['samples'])
def type_decider(self) -> str:
"""
@@ -91,7 +89,7 @@ class SheetParser(object):
def parse_info(self):
"""
_summary_
Pulls basic information from the excel sheet
"""
info = InfoParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_info()
parser_query = f"parse_{self.sub['submission_type']['value'].replace(' ', '_').lower()}"
@@ -101,14 +99,23 @@ class SheetParser(object):
except AttributeError:
logger.error(f"Couldn't find submission parser: {parser_query}")
for k,v in info.items():
if k != "sample":
self.sub[k] = v
match k:
case "sample":
pass
case _:
self.sub[k] = v
logger.debug(f"Parser.sub after info scrape: {pprint.pformat(self.sub)}")
def parse_reagents(self):
"""
Pulls reagent info from the excel sheet
"""
self.sub['reagents'] = ReagentParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type'], extraction_kit=self.sub['extraction_kit']).parse_reagents()
def parse_samples(self):
"""
Pulls sample info from the excel sheet
"""
self.sample_result, self.sub['samples'] = SampleParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_samples()
def parse_bacterial_culture(self, input_dict) -> dict:
@@ -159,7 +166,7 @@ class SheetParser(object):
Returns:
List[PydReagent]: List of reagents
"""
if not check_not_nan(self.sub['extraction_kit']):
if not check_not_nan(self.sub['extraction_kit']['value']):
dlg = KitSelector(ctx=self.ctx, title="Kit Needed", message="At minimum a kit is needed. Please select one.")
if dlg.exec():
self.sub['extraction_kit'] = dict(value=dlg.getValues(), parsed=False)
@@ -197,7 +204,16 @@ class InfoParser(object):
self.xl = xl
logger.debug(f"Info map for InfoParser: {pprint.pformat(self.map)}")
def fetch_submission_info_map(self, submission_type:dict) -> dict:
def fetch_submission_info_map(self, submission_type:str|dict) -> dict:
"""
Gets location of basic info from the submission_type object in the database.
Args:
submission_type (str|dict): name of the submission type or parsed object with value=submission_type
Returns:
dict: Location map of all info for this submission type
"""
if isinstance(submission_type, str):
submission_type = dict(value=submission_type, parsed=False)
logger.debug(f"Looking up submission type: {submission_type['value']}")
@@ -206,6 +222,12 @@ class InfoParser(object):
return info_map
def parse_info(self) -> dict:
"""
Pulls basic info from the excel sheet.
Returns:
dict: key:value of basic info
"""
dicto = {}
for sheet in self.xl.sheet_names:
df = self.xl.parse(sheet, header=None)
@@ -302,6 +324,8 @@ class SampleParser(object):
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type)
self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
if "plates" in sample_info_map:
self.plates = sample_info_map['plates']
self.excel_to_db_map = sample_info_map['xl_db_translation']
self.create_basic_dictionaries_from_plate_map()
if isinstance(self.lookup_table, pd.DataFrame):
@@ -383,7 +407,7 @@ class SampleParser(object):
sample[k] = v
logger.debug(f"Output sample dict: {sample}")
def parse_samples(self) -> List[dict]:
def parse_samples(self, generate:bool=True) -> List[dict]:
result = None
new_samples = []
for ii, sample in enumerate(self.samples):
@@ -414,7 +438,10 @@ class SampleParser(object):
translated_dict = custom_parser(translated_dict)
except AttributeError:
logger.error(f"Couldn't get custom parser: {parser_query}")
new_samples.append(self.generate_sample_object(translated_dict))
if generate:
new_samples.append(self.generate_sample_object(translated_dict))
else:
new_samples.append(translated_dict)
return result, new_samples
def generate_sample_object(self, input_dict) -> models.BasicSample:
@@ -464,6 +491,7 @@ class SampleParser(object):
dict: Updated sample dictionary
"""
logger.debug(f"Called wastewater sample parser")
return input_dict
def parse_wastewater_artic_sample(self, input_dict:dict) -> dict:
"""
@@ -481,6 +509,24 @@ class SampleParser(object):
# at the end, this has to be done here. No moving to sqlalchemy object :(
input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
return input_dict
def parse_first_strand_sample(self, input_dict:dict) -> dict:
logger.debug("Called first strand sample parser")
input_dict['well'] = re.search(r"\s\((.*)\)$", input_dict['submitter_id']).groups()[0]
input_dict['submitter_id'] = re.sub(r"\s\(.*\)$", "", str(input_dict['submitter_id'])).strip()
return input_dict
def grab_plates(self):
plates = []
for plate in self.plates:
df = self.xl.parse(plate['sheet'], header=None)
if isinstance(df.iat[plate['row']-1, plate['column']-1], str):
output = RSLNamer(ctx=self.ctx, instr=df.iat[plate['row']-1, plate['column']-1]).parsed_name
else:
continue
plates.append(output)
return plates
class PCRParser(object):
"""