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Everything working pretty well.

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This commit is contained in:
Landon Wark
2024-02-20 14:36:58 -06:00
parent a7e915995e
commit 1e711149f1
14 changed files with 62 additions and 37 deletions
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29
src/submissions/backend/db/models/kits.py
View File

@@ -4,10 +4,10 @@ All kit and reagent related models
from __future__ import annotations
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result, Settings
from tools import check_authorization, setup_lookup, Report, Result
from typing import List
from pandas import ExcelFile
from pathlib import Path
@@ -921,23 +921,32 @@ class SubmissionReagentAssociation(BaseClass):
from . import BasicSubmission
query: Query = cls.__database_session__.query(cls)
match reagent:
case Reagent():
case Reagent() | str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
if isinstance(reagent, str):
reagent = Reagent.query(lot_number=reagent)
query = query.filter(cls.reagent==reagent)
case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
query = query.join(Reagent).filter(Reagent.lot==reagent)
# case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
# query = query.filter(cls.reagent==reagent)
# logger.debug(f"Result: {query.all()}")
case _:
pass
match submission:
case BasicSubmission():
case BasicSubmission() | str():
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
query = query.filter(cls.submission==submission)
case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
query = query.join(BasicSubmission).filter(BasicSubmission.rsl_plate_num==submission)
# case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
# submission = BasicSubmission.query(rsl_number=submission)
# query = query.filter(cls.submission==submission)
# logger.debug(f"Result: {query.all()}")
case int():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission id {submission}")
submission = BasicSubmission.query(id=submission)
query = query.join(BasicSubmission).filter(BasicSubmission.id==submission)
case _:
pass

22
src/submissions/backend/db/models/submissions.py
View File

@@ -338,7 +338,7 @@ class BasicSubmission(BaseClass):
logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment']:
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number']:
try:
df = df.drop(item, axis=1)
except:
@@ -1068,7 +1068,21 @@ class BacterialCulture(BasicSubmission):
outstr = re.sub(r"BC(\d{6})", r"BC-\1", outstr, flags=re.IGNORECASE)
except (AttributeError, TypeError) as e:
outstr = RSLNamer.construct_new_plate_name(data=data)
return outstr
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
# logger.debug(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
# logger.debug(f"After addition of plate number the plate name is: {outstr}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
# return outstr
@classmethod
def get_regex(cls) -> str:
@@ -1078,7 +1092,7 @@ class BacterialCulture(BasicSubmission):
Returns:
str: string for regex construction
"""
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def filename_template(cls):
@@ -1244,7 +1258,7 @@ class Wastewater(BasicSubmission):
Returns:
str: String for regex construction
"""
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:

2
src/submissions/backend/excel/parser.py
View File

@@ -601,5 +601,3 @@ class PCRParser(object):
self.pcr['plugin'] = df.iloc[19][1]
self.pcr['exported_on'] = df.iloc[20][1]
self.pcr['imported_by'] = getuser()

8
src/submissions/backend/excel/reports.py
View File

@@ -32,7 +32,6 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
df = df.sort_values(['Submitting Lab', "Submitted Date"])
return df, df2
def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
"""
@@ -74,7 +73,6 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
html = temp.render(input=dicto)
return html
def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFrame:
"""
Convert list of control records to dataframe
@@ -104,7 +102,6 @@ def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFram
df = df_column_renamer(df=df)
return df
def df_column_renamer(df:DataFrame) -> DataFrame:
"""
Ad hoc function I created to clarify some fields
@@ -123,7 +120,6 @@ def df_column_renamer(df:DataFrame) -> DataFrame:
"kraken_percent":"kraken2_read_percent_(top_50)"
})
def displace_date(df:DataFrame) -> DataFrame:
"""
This function serves to split samples that were submitted on the same date by incrementing dates.
@@ -182,7 +178,6 @@ def check_date(df:DataFrame, item:dict, previous_dates:list) -> Tuple[DataFrame,
df, previous_dates = check_date(df, item, previous_dates)
return df, previous_dates
def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
"""
get all unique values in a dataframe column by name
@@ -196,7 +191,6 @@ 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:Settings, df: DataFrame) -> DataFrame:
"""
Removes semi-duplicates from dataframe after finding sequencing repeats.
@@ -227,4 +221,4 @@ def make_hitpicks(input:List[dict]) -> DataFrame:
Returns:
DataFrame: constructed dataframe.
"""
return DataFrame.from_records(input)
return DataFrame.from_records(input)

4
src/submissions/backend/validators/__init__.py
View File

@@ -133,10 +133,10 @@ class RSLNamer(object):
else:
today = data['submitted_date']
else:
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
try:
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
today = parse(today.group())
except AttributeError:
except (AttributeError, KeyError):
today = datetime.now()
if "rsl_plate_num" in data.keys():
plate_number = data['rsl_plate_num'].split("-")[-1][0]

9
src/submissions/backend/validators/pydant.py
View File

@@ -642,7 +642,14 @@ class PydSubmission(BaseModel, extra='allow'):
new_item = {}
new_item['type'] = k
new_item['location'] = excel_map['info'][k]
new_item['value'] = v['value']
match k:
case "comment":
if v['value'] is not None:
new_item['value'] = "--".join([comment['text'] for comment in v['value']])
else:
new_item['value'] = None
case _:
new_item['value'] = v['value']
new_info.append(new_item)
except KeyError:
logger.error(f"Unable to fill in {k}, not found in relevant info.")