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Large scale frontend refactor

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This commit is contained in:
Landon Wark
2023-11-14 11:16:54 -06:00
parent bf4149b1b3
commit da714c355d
26 changed files with 2682 additions and 2447 deletions
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19
src/submissions/backend/excel/parser.py
View File

@@ -2,7 +2,7 @@
contains parser object for pulling values from client generated submission sheets.
'''
from getpass import getuser
import pprint
from pprint import pformat
from typing import List
import pandas as pd
import numpy as np
@@ -15,7 +15,7 @@ import re
from datetime import date
from dateutil.parser import parse, ParserError
from tools import check_not_nan, convert_nans_to_nones, Settings
from frontend.custom_widgets.pop_ups import KitSelector
logger = logging.getLogger(f"submissions.{__name__}")
@@ -70,7 +70,7 @@ class SheetParser(object):
pass
case _:
self.sub[k] = v
logger.debug(f"Parser.sub after info scrape: {pprint.pformat(self.sub)}")
logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
def parse_reagents(self, extraction_kit:str|None=None):
"""
@@ -100,6 +100,7 @@ class SheetParser(object):
Returns:
List[PydReagent]: List of reagents
"""
from frontend.widgets.pop_ups import KitSelector
if not check_not_nan(self.sub['extraction_kit']['value']):
dlg = KitSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.")
if dlg.exec():
@@ -117,7 +118,7 @@ class SheetParser(object):
# kit = lookup_kit_types(ctx=self.ctx, name=self.sub['extraction_kit']['value'])
kit = KitType.query(name=self.sub['extraction_kit']['value'])
allowed_reagents = [item.name for item in kit.get_reagents()]
logger.debug(f"List of reagents for comparison with allowed_reagents: {pprint.pformat(self.sub['reagents'])}")
logger.debug(f"List of reagents for comparison with allowed_reagents: {pformat(self.sub['reagents'])}")
# self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent['value'].type in allowed_reagents]
self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent.type in allowed_reagents]
@@ -133,7 +134,7 @@ class SheetParser(object):
Returns:
PydSubmission: output pydantic model
"""
logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pprint.pformat(self.sub)}")
logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
psm = PydSubmission(filepath=self.filepath, **self.sub)
# delattr(psm, "filepath")
return psm
@@ -145,7 +146,7 @@ class InfoParser(object):
# self.ctx = ctx
self.map = self.fetch_submission_info_map(submission_type=submission_type)
self.xl = xl
logger.debug(f"Info map for InfoParser: {pprint.pformat(self.map)}")
logger.debug(f"Info map for InfoParser: {pformat(self.map)}")
def fetch_submission_info_map(self, submission_type:str|dict) -> dict:
@@ -186,7 +187,7 @@ class InfoParser(object):
continue
if sheet in self.map[k]['sheets']:
relevant[k] = v
logger.debug(f"relevant map for {sheet}: {pprint.pformat(relevant)}")
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}:
continue
for item in relevant:
@@ -236,7 +237,7 @@ class ReagentParser(object):
df = self.xl.parse(sheet, header=None, dtype=object)
df.replace({np.nan: None}, inplace = True)
relevant = {k.strip():v for k,v in self.map.items() if sheet in self.map[k]['sheet']}
logger.debug(f"relevant map for {sheet}: {pprint.pformat(relevant)}")
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}:
continue
for item in relevant:
@@ -302,7 +303,7 @@ class SampleParser(object):
logger.debug(f"Looking up submission type: {submission_type}")
# submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type)
submission_type = SubmissionType.query(name=submission_type)
logger.debug(f"info_map: {pprint.pformat(submission_type.info_map)}")
logger.debug(f"info_map: {pformat(submission_type.info_map)}")
sample_info_map = submission_type.info_map['samples']
# self.custom_parser = get_polymorphic_subclass(models.BasicSubmission, submission_type.name).parse_samples
self.custom_sub_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_samples

6
src/submissions/backend/excel/reports.py
View File

@@ -6,7 +6,7 @@ import logging
from datetime import date, timedelta
import re
from typing import Tuple
from tools import jinja_template_loading
from tools import jinja_template_loading, Settings
logger = logging.getLogger(f"submissions.{__name__}")
@@ -198,7 +198,7 @@ def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
return sorted(df[column_name].unique())
def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
def drop_reruns_from_df(ctx:Settings, df: DataFrame) -> DataFrame:
"""
Removes semi-duplicates from dataframe after finding sequencing repeats.
@@ -211,7 +211,7 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
"""
if 'rerun_regex' in ctx:
sample_names = get_unique_values_in_df_column(df, column_name="name")
rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
rerun_regex = re.compile(fr"{ctx.rerun_regex}")
for sample in sample_names:
if rerun_regex.search(sample):
first_run = re.sub(rerun_regex, "", sample)