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Improved form regeneration for artic.

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This commit is contained in:
Landon Wark
2024-01-04 13:29:18 -06:00
parent c688aa160c
commit 19448cc8f3
18 changed files with 519 additions and 123 deletions
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126
src/submissions/backend/db/models/submissions.py
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@@ -4,8 +4,9 @@ Models for the main submission types.
from __future__ import annotations
from getpass import getuser
import math, json, logging, uuid, tempfile, re, yaml
from operator import attrgetter
from pprint import pformat
from . import Reagent, SubmissionType, KitType, Organization, Equipment, SubmissionEquipmentAssociation
from . import Reagent, SubmissionType, KitType, Organization
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from json.decoder import JSONDecodeError
@@ -13,7 +14,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
import pandas as pd
from openpyxl import Workbook
from . import BaseClass
from tools import check_not_nan, row_map, query_return, setup_lookup
from tools import check_not_nan, row_map, query_return, setup_lookup, jinja_template_loading
from datetime import datetime, date
from typing import List
from dateutil.parser import parse
@@ -137,21 +138,23 @@ class BasicSubmission(BaseClass):
reagents = None
# samples = [item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num) for item in self.submission_sample_associations]
samples = [item.to_sub_dict() for item in self.submission_sample_associations]
try:
equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
if len(equipment) == 0:
equipment = None
except Exception as e:
logger.error(f"Error setting equipment: {self.equipment}")
equipment = None
else:
reagents = None
samples = None
equipment = None
try:
comments = self.comment
except Exception as e:
logger.error(f"Error setting comment: {self.comment}")
comments = None
try:
equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
if len(equipment) == 0:
equipment = None
except Exception as e:
logger.error(f"Error setting equipment: {self.equipment}")
equipment = None
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
@@ -508,7 +511,7 @@ class BasicSubmission(BaseClass):
field_value = len(self.samples)
else:
field_value = value
case "ctx" | "csv" | "filepath":
case "ctx" | "csv" | "filepath" | "equipment":
return
case "comment":
if value == "" or value == None or value == 'null':
@@ -552,8 +555,9 @@ class BasicSubmission(BaseClass):
Returns:
PydSubmission: converted object.
"""
from backend.validators import PydSubmission, PydSample, PydReagent
from backend.validators import PydSubmission, PydSample, PydReagent, PydEquipment
dicto = self.to_dict(full_data=True)
logger.debug(f"Backup dictionary: {pformat(dicto)}")
# dicto['filepath'] = Path(tempfile.TemporaryFile().name)
new_dict = {}
for key, value in dicto.items():
@@ -562,6 +566,8 @@ class BasicSubmission(BaseClass):
new_dict[key] = [PydReagent(**reagent) for reagent in value]
case "samples":
new_dict[key] = [PydSample(**sample) for sample in dicto['samples']]
case "equipment":
new_dict[key] = [PydEquipment(**equipment) for equipment in dicto['equipment']]
case "Plate Number":
new_dict['rsl_plate_num'] = dict(value=value, missing=True)
case "Submitter Plate Number":
@@ -576,19 +582,20 @@ class BasicSubmission(BaseClass):
# sys.exit()
return PydSubmission(**new_dict)
def backup(self, fname:Path):
def backup(self, fname:Path, full_backup:bool=True):
"""
Exports xlsx and yml info files for this instance.
Args:
fname (Path): Filename of xlsx file.
"""
backup = self.to_dict(full_data=True)
try:
with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
yaml.dump(backup, f)
except KeyError as e:
logger.error(f"Problem saving yml backup file: {e}")
if full_backup:
backup = self.to_dict(full_data=True)
try:
with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
yaml.dump(backup, f)
except KeyError as e:
logger.error(f"Problem saving yml backup file: {e}")
pyd = self.to_pydantic()
wb = pyd.autofill_excel()
wb = pyd.autofill_samples(wb)
@@ -766,6 +773,8 @@ class BasicSubmission(BaseClass):
msg = "This submission already exists.\nWould you like to overwrite?"
return instance, code, msg
def get_used_equipment(self) -> List[str]:
return [item.role for item in self.submission_equipment_associations]
# Below are the custom submission types
@@ -882,7 +891,8 @@ class BacterialCulture(BasicSubmission):
Returns:
str: string for regex construction
"""
return "(?P<Bacterial_Culture>RSL-?\\d{2}-?\\d{4})"
# return "(?P<Bacterial_Culture>RSL-?\\d{2}-?\\d{4})"
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
@classmethod
def filename_template(cls):
@@ -1175,7 +1185,36 @@ class WastewaterArtic(BasicSubmission):
logger.error(f"Couldn't construct df due to {e}")
input_dict['csv'] = df
return input_dict
@classmethod
def custom_autofill(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
input_excel = super().custom_autofill(input_excel, info, backup)
worksheet = input_excel["First Strand List"]
samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
samples = sorted(samples, key=attrgetter('column', 'row'))
source_plates = []
first_samples = []
for sample in samples:
sample = sample.sample
try:
assoc = [item.submission.rsl_plate_num for item in sample.sample_submission_associations if item.submission.submission_type_name=="Wastewater"][-1]
except IndexError:
logger.error(f"Association not found for {sample}")
continue
if assoc not in source_plates:
source_plates.append(assoc)
first_samples.append(sample.ww_processing_num)
# Pad list to length of 3
# source_plates = list(set(source_plates))
source_plates += ['None'] * (3 - len(source_plates))
first_samples += [''] * (3 - len(first_samples))
source_plates = zip(source_plates, first_samples, strict=False)
for iii, plate in enumerate(source_plates, start=8):
logger.debug(f"Plate: {plate}")
for jjj, value in enumerate(plate, start=3):
worksheet.cell(row=iii, column=jjj, value=value)
return input_excel
# Sample Classes
class BasicSample(BaseClass):
@@ -1286,11 +1325,15 @@ class BasicSample(BaseClass):
dict: dictionary of sample id, row and column in elution plate
"""
# Since there is no PCR, negliable result is necessary.
assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
tooltip_text = f"""
Sample name: {self.submitter_id}<br>
Well: {row_map[assoc.row]}{assoc.column}
"""
# assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
fields = self.to_sub_dict(submission_rsl=submission_rsl)
env = jinja_template_loading()
template = env.get_template("tooltip.html")
tooltip_text = template.render(fields=fields)
# tooltip_text = f"""
# Sample name: {self.submitter_id}<br>
# Well: {row_map[assoc.row]}{assoc.column}
# """
return dict(name=self.submitter_id[:10], positive=False, tooltip=tooltip_text)
@classmethod
@@ -1436,6 +1479,7 @@ class BasicSample(BaseClass):
used_class = cls.find_subclasses(attrs=kwargs, sample_type=sample_type)
instance = used_class(**kwargs)
instance.sample_type = sample_type
logger.debug(f"Creating instance: {instance}")
return instance
def save(self):
@@ -1523,6 +1567,25 @@ class WastewaterSample(BasicSample):
del output_dict['collection_date']
return output_dict
def to_sub_dict(self, submission_rsl: str | BasicSubmission) -> dict:
sample = super().to_sub_dict(submission_rsl)
if self.ww_processing_num != None:
sample['ww_processing_num'] = self.ww_processing_num
else:
sample['ww_processing_num'] = self.submitter_id
try:
assoc = [item for item in self.sample_submission_associations if item.submission.submission_type_name=="Wastewater"][-1]
except:
assoc = None
if assoc != None:
try:
sample['ct'] = f"{assoc.ct_n1:.2f}, {assoc.ct_n2:.2f}"
except TypeError:
sample['ct'] = "None, None"
sample['source_plate'] = assoc.submission.rsl_plate_num
sample['source_well'] = f"{row_map[assoc.row]}{assoc.column}"
return sample
class BacterialCultureSample(BasicSample):
"""
base of bacterial culture sample
@@ -1541,7 +1604,9 @@ class BacterialCultureSample(BasicSample):
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
"""
sample = super().to_sub_dict(submission_rsl=submission_rsl)
sample['name'] = f"{self.submitter_id} - ({self.organism})"
sample['name'] = self.submitter_id
sample['organism'] = self.organism
sample['concentration'] = self.concentration
return sample
def to_hitpick(self, submission_rsl: str | None = None) -> dict | None:
@@ -1622,13 +1687,15 @@ class SubmissionSampleAssociation(BaseClass):
if isinstance(polymorphic_identity, dict):
polymorphic_identity = polymorphic_identity['value']
if polymorphic_identity == None:
return cls
output = cls
else:
try:
return [item for item in cls.__subclasses__() if item.__mapper_args__['polymorphic_identity']==polymorphic_identity][0]
output = [item for item in cls.__subclasses__() if item.__mapper_args__['polymorphic_identity']==polymorphic_identity][0]
except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
return cls
output = cls
logger.debug(f"Using SubmissionSampleAssociation subclass: {output}")
return output
@classmethod
@setup_lookup
@@ -1707,6 +1774,7 @@ class SubmissionSampleAssociation(BaseClass):
Returns:
SubmissionSampleAssociation: Queried or new association.
"""
logger.debug(f"Attempting create or query with {kwargs}")
match submission:
case BasicSubmission():
pass