Pre-removal of constructors module.
This commit is contained in:
Landon Wark
@@ -13,7 +13,6 @@ from json.decoder import JSONDecodeError
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from math import ceil
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from sqlalchemy.ext.associationproxy import association_proxy
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import uuid
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from pandas import Timestamp
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from dateutil.parser import parse
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import re
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import pandas as pd
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@@ -301,6 +300,7 @@ class BasicSubmission(Base):
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@classmethod
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def enforce_name(cls, ctx:Settings, instr:str) -> str:
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logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
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logger.debug(f"Attempting enforcement on {instr}")
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return instr
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@classmethod
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@@ -344,6 +344,11 @@ class BasicSubmission(Base):
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logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
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return []
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def save(self, ctx:Settings):
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self.uploaded_by = getuser()
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ctx.database_session.add(self)
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ctx.database_session.commit()
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# Below are the custom submission types
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class BacterialCulture(BasicSubmission):
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@@ -536,6 +541,8 @@ class Wastewater(BasicSubmission):
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def construct():
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today = datetime.now()
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return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
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if outstr == None:
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outstr = construct()
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try:
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outstr = re.sub(r"PCR(-|_)", "", outstr)
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except AttributeError as e:
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@@ -743,6 +750,11 @@ class BasicSample(Base):
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logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
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return cls
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@classmethod
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def parse_sample(cls, input_dict:dict) -> dict:
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logger.debug(f"Called {cls.__name__} sample parser")
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return input_dict
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class WastewaterSample(BasicSample):
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"""
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Derivative wastewater sample
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@@ -757,51 +769,51 @@ class WastewaterSample(BasicSample):
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__mapper_args__ = {"polymorphic_identity": "Wastewater Sample", "polymorphic_load": "inline"}
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@validates("collected-date")
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def convert_cdate_time(self, key, value):
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logger.debug(f"Validating {key}: {value}")
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if isinstance(value, Timestamp):
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return value.date()
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if isinstance(value, str):
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return parse(value)
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return value
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# @validates("collected-date")
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# def convert_cdate_time(self, key, value):
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# logger.debug(f"Validating {key}: {value}")
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# if isinstance(value, Timestamp):
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# return value.date()
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# if isinstance(value, str):
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# return parse(value)
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# return value
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@validates("rsl_number")
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def use_submitter_id(self, key, value):
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logger.debug(f"Validating {key}: {value}")
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return value or self.submitter_id
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# @validates("rsl_number")
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# def use_submitter_id(self, key, value):
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# logger.debug(f"Validating {key}: {value}")
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# return value or self.submitter_id
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def set_attribute(self, name:str, value):
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"""
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Set an attribute of this object. Extends parent.
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# def set_attribute(self, name:str, value):
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# """
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# Set an attribute of this object. Extends parent.
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Args:
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name (str): name of the attribute
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value (_type_): value to be set
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"""
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# Due to the plate map being populated with RSL numbers, we have to do some shuffling.
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match name:
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case "submitter_id":
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# If submitter_id already has a value, stop
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if self.submitter_id != None:
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return
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# otherwise also set rsl_number to the same value
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else:
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super().set_attribute("rsl_number", value)
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case "ww_full_sample_id":
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# If value present, set ww_full_sample_id and make this the submitter_id
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if value != None:
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super().set_attribute(name, value)
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name = "submitter_id"
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case 'collection_date':
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# If this is a string use dateutils to parse into date()
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if isinstance(value, str):
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logger.debug(f"collection_date {value} is a string. Attempting parse...")
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value = parse(value)
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case "rsl_number":
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if value == None:
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value = self.submitter_id
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super().set_attribute(name, value)
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# Args:
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# name (str): name of the attribute
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# value (_type_): value to be set
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# """
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# # Due to the plate map being populated with RSL numbers, we have to do some shuffling.
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# match name:
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# case "submitter_id":
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# # If submitter_id already has a value, stop
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# if self.submitter_id != None:
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# return
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# # otherwise also set rsl_number to the same value
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# else:
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# super().set_attribute("rsl_number", value)
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# case "ww_full_sample_id":
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# # If value present, set ww_full_sample_id and make this the submitter_id
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# if value != None:
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# super().set_attribute(name, value)
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# name = "submitter_id"
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# case 'collection_date':
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# # If this is a string use dateutils to parse into date()
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# if isinstance(value, str):
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# logger.debug(f"collection_date {value} is a string. Attempting parse...")
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# value = parse(value)
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# case "rsl_number":
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# if value == None:
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# value = self.submitter_id
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# super().set_attribute(name, value)
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def to_hitpick(self, submission_rsl:str) -> dict|None:
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"""
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@@ -832,6 +844,16 @@ class WastewaterSample(BasicSample):
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except IndexError:
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return None
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@classmethod
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def parse_sample(cls, input_dict: dict) -> dict:
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output_dict = super().parse_sample(input_dict)
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if output_dict['rsl_number'] == None:
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output_dict['rsl_number'] = output_dict['submitter_id']
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if output_dict['ww_full_sample_id'] != None:
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output_dict["submitter_id"] = output_dict['ww_full_sample_id']
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return output_dict
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class BacterialCultureSample(BasicSample):
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"""
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base of bacterial culture sample
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@@ -873,7 +895,7 @@ class SubmissionSampleAssociation(Base):
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# Refers to the type of parent.
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# Hooooooo boy, polymorphic association type, now we're getting into the weeds!
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__mapper_args__ = {
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"polymorphic_identity": "basic_association",
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"polymorphic_identity": "Basic Association",
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"polymorphic_on": base_sub_type,
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"with_polymorphic": "*",
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}
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@@ -886,6 +908,19 @@ class SubmissionSampleAssociation(Base):
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def __repr__(self) -> str:
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return f"<SubmissionSampleAssociation({self.submission.rsl_plate_num} & {self.sample.submitter_id})"
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@classmethod
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def find_polymorphic_subclass(cls, polymorphic_identity:str|None=None):
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if isinstance(polymorphic_identity, dict):
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polymorphic_identity = polymorphic_identity['value']
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if polymorphic_identity == None:
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return cls
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else:
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try:
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return [item for item in cls.__subclasses__() if item.__mapper_args__['polymorphic_identity']==polymorphic_identity][0]
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except Exception as e:
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logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
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return cls
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class WastewaterAssociation(SubmissionSampleAssociation):
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"""
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@@ -897,5 +932,5 @@ class WastewaterAssociation(SubmissionSampleAssociation):
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n2_status = Column(String(32)) #: positive or negative for N2
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pcr_results = Column(JSON) #: imported PCR status from QuantStudio
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__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
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__mapper_args__ = {"polymorphic_identity": "Wastewater Association", "polymorphic_load": "inline"}
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