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Increased robustness of form parsers.

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This commit is contained in:
Landon Wark
2023-10-06 14:22:59 -05:00
parent e484eabb22
commit 1b6d415788
27 changed files with 747 additions and 284 deletions
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4
src/submissions/backend/db/models/__init__.py
View File

@@ -2,11 +2,11 @@
Contains all models for sqlalchemy
'''
from typing import Any
from sqlalchemy.orm import declarative_base
from sqlalchemy.orm import declarative_base, DeclarativeMeta
import logging
from pprint import pformat
Base = declarative_base()
Base: DeclarativeMeta = declarative_base()
metadata = Base.metadata
logger = logging.getLogger(f"submissions.{__name__}")

5
src/submissions/backend/db/models/kits.py
View File

@@ -332,4 +332,7 @@ class SubmissionTypeKitTypeAssociation(Base):
self.constant_cost = 0.00
def __repr__(self) -> str:
return f"<SubmissionTypeKitTypeAssociation({self.submission_type.name})"
return f"<SubmissionTypeKitTypeAssociation({self.submission_type.name})"
def set_attrib(self, name, value):
self.__setattr__(name, value)

122
src/submissions/backend/db/models/submissions.py
View File

@@ -13,6 +13,9 @@ from sqlalchemy.ext.associationproxy import association_proxy
import uuid
from pandas import Timestamp
from dateutil.parser import parse
import re
import pandas as pd
from tools import row_map
logger = logging.getLogger(f"submissions.{__name__}")
@@ -43,6 +46,7 @@ class BasicSubmission(Base):
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
comment = Column(JSON)
submission_category = Column(String(64))
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
@@ -83,7 +87,7 @@ class BasicSubmission(Base):
dict: dictionary used in submissions summary and details
"""
# get lab from nested organization object
logger.debug(f"Converting {self.rsl_plate_num} to dict...")
# logger.debug(f"Converting {self.rsl_plate_num} to dict...")
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -125,6 +129,7 @@ class BasicSubmission(Base):
"id": self.id,
"Plate Number": self.rsl_plate_num,
"Submission Type": self.submission_type_name,
"Submission Category": self.submission_category,
"Submitter Plate Number": self.submitter_plate_num,
"Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
"Submitting Lab": sub_lab,
@@ -232,6 +237,34 @@ class BasicSubmission(Base):
else:
continue
return output_list
@classmethod
def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
"""
Update submission dictionary with type specific information
Args:
input_dict (dict): Input sample dictionary
Returns:
dict: Updated sample dictionary
"""
logger.debug(f"Calling {cls.__name__} info parser.")
return input_dict
@classmethod
def parse_samples(cls, input_dict:dict) -> dict:
"""
Update sample dictionary with type specific information
Args:
input_dict (dict): Input sample dictionary
Returns:
dict: Updated sample dictionary
"""
logger.debug(f"Called {cls.__name__} sample parser")
return input_dict
# Below are the custom submission types
@@ -252,7 +285,7 @@ class BacterialCulture(BasicSubmission):
output = super().to_dict(full_data=full_data)
if full_data:
output['controls'] = [item.to_sub_dict() for item in self.controls]
return output
return output
class Wastewater(BasicSubmission):
"""
@@ -278,6 +311,23 @@ class Wastewater(BasicSubmission):
output['Technician'] = f"Enr: {self.technician}, Ext: {self.ext_technician}, PCR: {self.pcr_technician}"
return output
@classmethod
def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
"""
Update submission dictionary with type specific information. Extends parent
Args:
input_dict (dict): Input sample dictionary
Returns:
dict: Updated sample dictionary
"""
input_dict = super().parse_info(input_dict)
if xl != None:
input_dict['csv'] = xl.parse("Copy to import file")
return input_dict
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
@@ -303,6 +353,25 @@ class WastewaterArtic(BasicSubmission):
except Exception as e:
logger.error(f"Calculation error: {e}")
@classmethod
def parse_samples(cls, input_dict: dict) -> dict:
"""
Update sample dictionary with type specific information. Extends parent.
Args:
input_dict (dict): Input sample dictionary
Returns:
dict: Updated sample dictionary
"""
input_dict = super().parse_samples(input_dict)
input_dict['sample_type'] = "Wastewater Sample"
# Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# 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
class BasicSample(Base):
"""
Base of basic sample which polymorphs into BCSample and WWSample
@@ -364,26 +433,31 @@ class BasicSample(Base):
Returns:
dict: 'well' and sample submitter_id as 'name'
"""
row_map = {1:"A", 2:"B", 3:"C", 4:"D", 5:"E", 6:"F", 7:"G", 8:"H"}
self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
sample = {}
try:
sample['well'] = f"{row_map[self.assoc.row]}{self.assoc.column}"
sample['well'] = f"{row_map[assoc.row]}{assoc.column}"
except KeyError as e:
logger.error(f"Unable to find row {self.assoc.row} in row_map.")
logger.error(f"Unable to find row {assoc.row} in row_map.")
sample['well'] = None
sample['name'] = self.submitter_id
return sample
def to_hitpick(self, submission_rsl:str|None=None) -> dict|None:
"""
Outputs a dictionary of locations
Outputs a dictionary usable for html plate maps.
Returns:
dict: dictionary of sample id, row and column in elution plate
"""
# Since there is no PCR, negliable result is necessary.
return dict(name=self.submitter_id, positive=False)
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}
"""
return dict(name=self.submitter_id, positive=False, tooltip=tooltip_text)
class WastewaterSample(BasicSample):
"""
@@ -445,42 +519,24 @@ class WastewaterSample(BasicSample):
value = self.submitter_id
super().set_attribute(name, value)
def to_sub_dict(self, submission_rsl:str) -> dict:
"""
Gui friendly dictionary. Extends parent method.
This version will include PCR status.
Args:
submission_rsl (str): RSL plate number (passed down from the submission.to_dict() functino)
Returns:
dict: Alphanumeric well id and sample name
"""
# Get the relevant submission association for this sample
sample = super().to_sub_dict(submission_rsl=submission_rsl)
# check if PCR data exists.
try:
check = self.assoc.ct_n1 != None and self.assoc.ct_n2 != None
except AttributeError as e:
check = False
if check:
sample['name'] = f"{self.submitter_id}\n\t- ct N1: {'{:.2f}'.format(self.assoc.ct_n1)} ({self.assoc.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.assoc.ct_n2)} ({self.assoc.n2_status})"
return sample
def to_hitpick(self, submission_rsl:str) -> dict|None:
"""
Outputs a dictionary of locations if sample is positive
Outputs a dictionary usable for html plate maps. Extends parent method.
Returns:
dict: dictionary of sample id, row and column in elution plate
"""
sample = super().to_hitpick(submission_rsl=submission_rsl)
assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
# if either n1 or n2 is positive, include this sample
try:
sample['positive'] = any(["positive" in item for item in [self.assoc.n1_status, self.assoc.n2_status]])
sample['positive'] = any(["positive" in item for item in [assoc.n1_status, assoc.n2_status]])
except (TypeError, AttributeError) as e:
logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
try:
sample['tooltip'] += f"<br>- ct N1: {'{:.2f}'.format(assoc.ct_n1)} ({assoc.n1_status})<br>- ct N2: {'{:.2f}'.format(assoc.ct_n2)} ({assoc.n2_status})"
except (TypeError, AttributeError) as e:
logger.error(f"Couldn't set tooltip for {self.rsl_number}. Looks like there isn't PCR data.")
return sample
class BacterialCultureSample(BasicSample):