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Improved generic submissions to replace viral culture addition.

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This commit is contained in:
lwark
2024-09-06 11:22:05 -05:00
parent bcb6e15449
commit 7f6a476cd7
11 changed files with 166 additions and 155 deletions
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2
src/submissions/backend/db/models/controls.py
View File

@@ -58,7 +58,7 @@ class ControlType(BaseClass):
Get subtypes associated with this controltype (currently used only for Kraken)
Args:
mode (str): analysis mode name
mode (str): analysis mode sub_type
Returns:
List[str]: list of subtypes available

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

@@ -5,7 +5,7 @@ from __future__ import annotations
import datetime
import json
from pprint import pprint
from pprint import pprint, pformat
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
@@ -846,7 +846,7 @@ class SubmissionType(BaseClass):
pass
return cls.execute_query(query=query, limit=limit)
def to_dict(self):
def to_export_dict(self):
base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export')
base_dict['defaults'] = self.defaults
@@ -874,6 +874,7 @@ class SubmissionType(BaseClass):
return None
with open(filepath, "r") as f:
import_dict = json.load(fp=f)
logger.debug(pformat(import_dict))
submission_type = cls.query(name=import_dict['name'])
if submission_type:
return submission_type

213
src/submissions/backend/db/models/submissions.py
View File

@@ -113,15 +113,6 @@ class BasicSubmission(BaseClass):
__mapper_args__ = {
"polymorphic_identity": "Basic Submission",
"polymorphic_on": submission_type_name,
# "polymorphic_on": case(
#
# (submission_type_name == "Bacterial Culture", "Bacterial Culture"),
# (submission_type_name == "Wastewater Artic", "Wastewater Artic"),
# (submission_type_name == "Wastewater", "Wastewater"),
# (submission_type_name == "Viral Culture", "Bacterial Culture"),
#
# else_="Basic Sample"
# ),
"with_polymorphic": "*",
}
@@ -160,7 +151,7 @@ class BasicSubmission(BaseClass):
return output
@classmethod
def get_default_info(cls, *args):
def get_default_info(cls, *args, submission_type: SubmissionType | None = None):
# NOTE: Create defaults for all submission_types
parent_defs = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
@@ -185,7 +176,10 @@ class BasicSubmission(BaseClass):
continue
else:
output[k] = v
st = cls.get_submission_type()
if isinstance(submission_type, SubmissionType):
st = submission_type
else:
st = cls.get_submission_type(submission_type)
if st is None:
logger.error("No default info for BasicSubmission.")
else:
@@ -205,18 +199,23 @@ class BasicSubmission(BaseClass):
return output
@classmethod
def get_submission_type(cls) -> SubmissionType:
def get_submission_type(cls, sub_type: str | SubmissionType | None = None) -> SubmissionType:
"""
Gets the SubmissionType associated with this class
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
"""
name = cls.__mapper_args__['polymorphic_identity']
return SubmissionType.query(name=name)
match sub_type:
case str():
return SubmissionType.query(name=sub_type)
case SubmissionType():
return sub_type
case _:
return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
@classmethod
def construct_info_map(cls, mode: Literal["read", "write"]) -> 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.
@@ -226,17 +225,17 @@ class BasicSubmission(BaseClass):
Returns:
dict: Map of info locations.
"""
return cls.get_submission_type().construct_info_map(mode=mode)
return cls.get_submission_type(submission_type).construct_info_map(mode=mode)
@classmethod
def construct_sample_map(cls) -> dict:
def construct_sample_map(cls, submission_type:SubmissionType|None=None) -> dict:
"""
Method to call submission type's construct_sample_map
Returns:
dict: sample location map
"""
return cls.get_submission_type().construct_sample_map()
return cls.get_submission_type(submission_type).construct_sample_map()
@classmethod
def finalize_details(cls, input_dict: dict) -> dict:
@@ -466,7 +465,7 @@ class BasicSubmission(BaseClass):
Returns:
pd.DataFrame: Pandas Dataframe of all relevant submissions
"""
# logger.debug(f"Querying Type: {submission_type}")
logger.debug(f"Querying Type: {submission_type}")
# logger.debug(f"Using limit: {limit}")
# NOTE: use lookup function to create list of dicts
subs = [item.to_dict() for item in
@@ -635,14 +634,13 @@ class BasicSubmission(BaseClass):
super().save()
@classmethod
def get_regex(cls) -> str:
"""
Dummy for inheritence.
Returns:
str: Regex for submission type.
"""
return cls.construct_regex()
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:
return cls.get_submission_type(submission_type).defaults['regex']
except AttributeError as e:
raise AttributeError(f"Couldn't get submission type for {cls.__mapper_args__['polymorphic_identity']}")
# Polymorphic functions
@@ -654,7 +652,8 @@ class BasicSubmission(BaseClass):
Returns:
re.Pattern: Regular expression pattern to discriminate between submission types.
"""
rstring = rf'{"|".join([item.get_regex() for item in cls.__subclasses__()])}'
# rstring = rf'{"|".join([item.get_regex() for item in cls.__subclasses__()])}'
rstring = rf'{"|".join([item.defaults["regex"] for item in SubmissionType.query()])}'
regex = re.compile(rstring, flags=re.IGNORECASE | re.VERBOSE)
return regex
@@ -685,7 +684,7 @@ 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}")
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:
@@ -796,11 +795,13 @@ class BasicSubmission(BaseClass):
# logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
from backend.validators import RSLNamer
# logger.debug(f"instr coming into {cls}: {instr}")
# logger.debug(f"data coming into {cls}: {data}")
defaults = cls.get_default_info("abbreviation", "submission_type")
data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type']
logger.debug(f"data coming into {cls}: {data}")
# defaults = cls.get_default_info("abbreviation", "submission_type")
data['abbreviation'] = cls.get_default_info("abbreviation", submission_type=data['submission_type'])
# logger.debug(f"Default info: {defaults}")
# data['abbreviation'] = defaults['abbreviation']
# if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
# data['submission_type'] = defaults['submission_type']
if instr in [None, ""]:
# logger.debug("Sending to RSLNamer to make new plate name.")
outstr = RSLNamer.construct_new_plate_name(data=data)
@@ -829,9 +830,11 @@ class BasicSubmission(BaseClass):
except AttributeError as e:
repeat = ""
outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
abb = cls.get_default_info('abbreviation')
outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
# abb = cls.get_default_info('abbreviation')
# outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
# return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
outstr = re.sub(rf"RSL{data['abbreviation']}", rf"RSL-{data['abbreviation']}", outstr)
return re.sub(rf"{data['abbreviation']}(\d)", rf"{data['abbreviation']}-\1", outstr)
@classmethod
def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
@@ -1261,15 +1264,15 @@ class BacterialCulture(BasicSubmission):
output['controls'] = [item.to_sub_dict() for item in self.controls]
return output
@classmethod
def get_regex(cls) -> str:
"""
Retrieves string for regex construction.
Returns:
str: string for regex construction
"""
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
# @classmethod
# def get_regex(cls) -> str:
# """
# Retrieves string for regex construction.
#
# Returns:
# str: string for regex construction
# """
# return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def filename_template(cls):
@@ -1339,47 +1342,47 @@ 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]|$)?R?\d?)?)"
@classmethod
def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
"""
Extends parent
"""
# logger.debug(f"Checking {sample.well}")
# logger.debug(f"here's the worksheet: {worksheet}")
row = super().custom_sample_autofill_row(sample, worksheet)
df = pd.DataFrame(list(worksheet.values))
# logger.debug(f"Here's the dataframe: {df}")
idx = df[df[0] == sample.well]
if idx.empty:
new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
# logger.debug(f"Checking: {new}")
idx = df[df[0] == new]
# logger.debug(f"Here is the row: {idx}")
row = idx.index.to_list()[0]
return row + 1
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
return input_dict
# class ViralCulture(BasicSubmission):
#
# id = Column(INTEGER, ForeignKey('_basicsubmission.id'), primary_key=True)
# __mapper_args__ = dict(polymorphic_identity="Viral Culture",
# polymorphic_load="inline",
# inherit_condition=(id == BasicSubmission.id))
#
# # @classmethod
# # def get_regex(cls) -> str:
# # """
# # Retrieves string for regex construction.
# #
# # Returns:
# # str: string for regex construction
# # """
# # return "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?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):
@@ -1499,15 +1502,15 @@ class Wastewater(BasicSubmission):
outstr = super().enforce_name(instr=instr, data=data)
return outstr
@classmethod
def get_regex(cls) -> str:
"""
Retrieves string for regex construction
Returns:
str: String for regex construction
"""
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
# @classmethod
# def get_regex(cls) -> str:
# """
# Retrieves string for regex construction
#
# Returns:
# str: String for regex construction
# """
# return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
@@ -1919,15 +1922,15 @@ class WastewaterArtic(BasicSubmission):
# logger.debug(f"Final EN name: {final_en_name}")
return final_en_name
@classmethod
def get_regex(cls) -> str:
"""
Retrieves string for regex construction
Returns:
str: string for regex construction.
"""
return "(?P<Wastewater_Artic>(\\d{4}-\\d{2}-\\d{2}(?:-|_)(?:\\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)\\d?(\\D|$)R?\\d?)?))"
# @classmethod
# def get_regex(cls) -> str:
# """
# Retrieves string for regex construction
#
# Returns:
# str: string for regex construction.
# """
# return "(?P<Wastewater_Artic>(\\d{4}-\\d{2}-\\d{2}(?:-|_)(?:\\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)\\d?(\\D|$)R?\\d?)?))"
@classmethod
def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None) -> dict:

11
src/submissions/backend/excel/parser.py
View File

@@ -76,6 +76,7 @@ class SheetParser(object):
# NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
if v not in [None, "None", "", " "]:
self.submission_type = SubmissionType.query(name=v)
logger.debug(f"Updated self.submission_type to {self.submission_type}")
case _:
self.sub[k] = v
@@ -202,7 +203,7 @@ class InfoParser(object):
"""
self.submission_type = dict(value=self.submission_type_obj.name, missing=True)
# logger.debug(f"Looking up submission type: {self.submission_type['value']}")
info_map = self.sub_object.construct_info_map("read")
info_map = self.sub_object.construct_info_map(submission_type=self.submission_type_obj, mode="read")
# NOTE: Get the parse_info method from the submission type specified
return info_map
@@ -385,10 +386,12 @@ class SampleParser(object):
self.xl = xl
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
logger.debug(f"Sample parser is using submission type: {submission_type}")
self.submission_type = submission_type.name
self.submission_type_obj = submission_type
if sub_object is None:
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type_obj.name)
logger.warning(f"Sample parser attempting to fetch submission class with polymorphic identity: {self.submission_type}")
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.sub_object = sub_object
self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
# logger.debug(f"sample_info_map: {self.sample_info_map}")
@@ -406,12 +409,12 @@ class SampleParser(object):
dict: Info locations.
"""
# logger.debug(f"Looking up submission type: {submission_type}")
self.sample_type = self.sub_object.get_default_info("sample_type")
self.sample_type = self.sub_object.get_default_info("sample_type", submission_type=submission_type)
self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)
# logger.debug(f"Got sample class: {self.samp_object.__name__}")
# logger.debug(f"info_map: {pformat(se)}")
if sample_map is None:
sample_info_map = self.sub_object.construct_sample_map()
sample_info_map = self.sub_object.construct_sample_map(submission_type=self.submission_type_obj)
else:
sample_info_map = sample_map
return sample_info_map

14
src/submissions/backend/validators/__init__.py
View File

@@ -26,11 +26,11 @@ class RSLNamer(object):
if self.submission_type is None:
# logger.debug("Creating submission type because none exists")
self.submission_type = self.retrieve_submission_type(filename=filename)
# logger.debug(f"got submission type: {self.submission_type}")
logger.debug(f"got submission type: {self.submission_type}")
if self.submission_type is not None:
# logger.debug("Retrieving BasicSubmission subclass")
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex())
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
if data is None:
data = dict(submission_type=self.submission_type)
if "submission_type" not in data.keys():
@@ -50,7 +50,7 @@ class RSLNamer(object):
"""
match filename:
case Path():
# logger.debug(f"Using path method for {filename}.")
logger.debug(f"Using path method for {filename}.")
if filename.exists():
wb = load_workbook(filename)
try:
@@ -70,12 +70,14 @@ class RSLNamer(object):
submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
case str():
regex = BasicSubmission.construct_regex()
# logger.debug(f"Using string method for {filename}.")
logger.debug(f"Using string method for {filename}.")
logger.debug(f"Using regex: {regex}")
m = regex.search(filename)
try:
submission_type = m.lastgroup
logger.debug(f"Got submission type: {submission_type}")
except AttributeError as e:
logger.critical(f"No RSL plate number found or submission type found!: {e}")
logger.critical(f"No submission type found or submission type found!: {e}")
case _:
submission_type = None
try:
@@ -112,7 +114,7 @@ class RSLNamer(object):
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
except re.error as e:
regex = BasicSubmission.construct_regex()
# logger.debug(f"Using regex: {regex}")
logger.debug(f"Using regex: {regex}")
match filename:
case Path():
m = regex.search(filename.stem)

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

@@ -509,7 +509,7 @@ class PydSubmission(BaseModel, extra='allow'):
if check_not_nan(value['value']):
return value
else:
# logger.debug("Constructing plate name.")
# logger.debug("Constructing plate sub_type.")
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
output = "RSL-BS-Test001"
else:
@@ -642,7 +642,7 @@ class PydSubmission(BaseModel, extra='allow'):
# this could also be done with default_factory
self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
def set_attribute(self, key: str, value):
"""