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Improved navigation and clarity in details view.

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lwark
2024-09-13 15:23:11 -05:00
parent 744394f236
commit c7d83401e7
15 changed files with 270 additions and 177 deletions
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12
src/submissions/backend/db/models/kits.py
View File

@@ -8,12 +8,13 @@ import json
from pprint import pprint, pformat
import yaml
from jinja2 import TemplateNotFound
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
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result
from tools import check_authorization, setup_lookup, Report, Result, jinja_template_loading
from typing import List, Literal, Generator, Any
from pandas import ExcelFile
from pathlib import Path
@@ -421,12 +422,13 @@ class Reagent(BaseClass):
else:
return f"<Reagent({self.role.name}-{self.lot})>"
def to_sub_dict(self, extraction_kit: KitType = None) -> dict:
def to_sub_dict(self, extraction_kit: KitType = None, full_data:bool=False) -> dict:
"""
dictionary containing values necessary for gui
Args:
extraction_kit (KitType, optional): KitType to use to get reagent type. Defaults to None.
full_data (bool, optional): Whether to include submissions in data for details. Defaults to False.
Returns:
dict: representation of the reagent's attributes
@@ -456,13 +458,17 @@ class Reagent(BaseClass):
place_holder = "NA"
else:
place_holder = place_holder.strftime("%Y-%m-%d")
return dict(
output = dict(
name=self.name,
role=rtype,
lot=self.lot,
expiry=place_holder,
missing=False
)
if full_data:
output['submissions'] = [sub.rsl_plate_num for sub in self.submissions]
output['excluded'] = ['missing', 'submissions', 'excluded']
return output
def update_last_used(self, kit: KitType) -> Report:
"""

65
src/submissions/backend/db/models/submissions.py
View File

@@ -168,7 +168,8 @@ class BasicSubmission(BaseClass):
'extraction_info', 'comment', 'barcode',
'platemap', 'export_map', 'equipment', 'tips'],
# NOTE: Fields not placed in ui form
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer', 'submission_object', "tips"] + recover,
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
'submission_object', "tips", 'contact_phone'] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover
)
@@ -229,7 +230,8 @@ class BasicSubmission(BaseClass):
return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
@classmethod
def construct_info_map(cls, submission_type:SubmissionType|None=None, mode: Literal["read", "write"]="read") -> dict:
def construct_info_map(cls, submission_type: SubmissionType | None = None,
mode: Literal["read", "write"] = "read") -> dict:
"""
Method to call submission type's construct info map.
@@ -242,7 +244,7 @@ class BasicSubmission(BaseClass):
return cls.get_submission_type(submission_type).construct_info_map(mode=mode)
@classmethod
def construct_sample_map(cls, submission_type:SubmissionType|None=None) -> dict:
def construct_sample_map(cls, submission_type: SubmissionType | None = None) -> dict:
"""
Method to call submission type's construct_sample_map
@@ -609,7 +611,7 @@ class BasicSubmission(BaseClass):
new_dict = {}
for key, value in dicto.items():
# logger.debug(f"Checking {key}")
missing = value is None or value in ['', 'None']
missing = value in ['', 'None', None]
match key:
case "reagents":
new_dict[key] = [PydReagent(**reagent) for reagent in value]
@@ -628,7 +630,7 @@ class BasicSubmission(BaseClass):
case "id":
pass
case _:
# logger.debug(f"Setting dict {key} to {value}")
logger.debug(f"Setting dict {key} to {value}")
new_dict[key.lower().replace(" ", "_")] = dict(value=value, missing=missing)
# logger.debug(f"{key} complete after {time()-start}")
new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
@@ -648,7 +650,7 @@ class BasicSubmission(BaseClass):
return super().save()
@classmethod
def get_regex(cls, submission_type:SubmissionType|str|None=None):
def get_regex(cls, submission_type: SubmissionType | str | None = None):
# logger.debug(f"Attempting to get regex for {cls.__mapper_args__['polymorphic_identity']}")
logger.debug(f"Attempting to get regex for {submission_type}")
try:
@@ -707,7 +709,8 @@ class BasicSubmission(BaseClass):
# item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
logger.error(
f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
case _:
pass
if attrs is None or len(attrs) == 0:
@@ -1199,6 +1202,8 @@ class BasicSubmission(BaseClass):
dlg = SubmissionComment(parent=obj, submission=self)
if dlg.exec():
comment = dlg.parse_form()
if comment in ["", None]:
return
self.set_attribute(key='comment', value=comment)
# logger.debug(self.comment)
self.save(original=False)
@@ -1368,49 +1373,6 @@ class BacterialCulture(BasicSubmission):
return input_dict
# class ViralCulture(BasicSubmission):
#
# id = Column(INTEGER, ForeignKey('_basicsubmission.id'), primary_key=True)
# __mapper_args__ = dict(polymorphic_identity="Viral Culture",
# polymorphic_load="inline",
# inherit_condition=(id == BasicSubmission.id))
#
# # @classmethod
# # def get_regex(cls) -> str:
# # """
# # Retrieves string for regex construction.
# #
# # Returns:
# # str: string for regex construction
# # """
# # return "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
#
# @classmethod
# def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
# """
# Extends parent
# """
# # logger.debug(f"Checking {sample.well}")
# # logger.debug(f"here's the worksheet: {worksheet}")
# row = super().custom_sample_autofill_row(sample, worksheet)
# df = pd.DataFrame(list(worksheet.values))
# # logger.debug(f"Here's the dataframe: {df}")
# idx = df[df[0] == sample.well]
# if idx.empty:
# new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
# # logger.debug(f"Checking: {new}")
# idx = df[df[0] == new]
# # logger.debug(f"Here is the row: {idx}")
# row = idx.index.to_list()[0]
# return row + 1
#
# @classmethod
# def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
# input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
# logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
# return input_dict
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
@@ -2239,6 +2201,9 @@ class BasicSample(BaseClass):
"""
gui friendly dictionary, extends parent method.
Args:
full_data (bool): Whether to use full object or truncated. Defaults to False
Returns:
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
"""