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new parsers/DB objects, pre code cleanup

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Landon Wark
2023-09-06 08:41:08 -05:00
parent bc7a3b8f5f
commit e0b80f6c7a
12 changed files with 263 additions and 137 deletions
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24
src/submissions/backend/db/models/submissions.py
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@@ -3,7 +3,7 @@ Models for the main submission types.
'''
import math
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT, BOOLEAN
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
from sqlalchemy.orm import relationship, validates
import logging
import json
@@ -106,7 +106,7 @@ class BasicSubmission(Base):
ext_info = None
logger.debug(f"Json error in {self.rsl_plate_num}: {e}")
try:
reagents = [item.to_sub_dict() for item in self.reagents]
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.reagents]
except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}")
reagents = None
@@ -252,6 +252,8 @@ class Wastewater(BasicSubmission):
"""
# samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
pcr_info = Column(JSON)
ext_technician = Column(String(64))
pcr_technician = Column(String(64))
# ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
__mapper_args__ = {"polymorphic_identity": "Wastewater", "polymorphic_load": "inline"}
@@ -267,6 +269,7 @@ class Wastewater(BasicSubmission):
output['pcr_info'] = json.loads(self.pcr_info)
except TypeError as e:
pass
output['Technician'] = f"Enr: {self.technician}, Ext: {self.ext_technician}, PCR: {self.pcr_technician}"
return output
class WastewaterArtic(BasicSubmission):
@@ -460,10 +463,10 @@ class WastewaterSample(BasicSample):
except AttributeError as e:
check = False
if check:
logger.debug(f"Using well info in name.")
# logger.debug(f"Using well info in name.")
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})"
else:
logger.error(f"Couldn't get the pcr info")
# else:
# logger.error(f"Couldn't get the pcr info")
return sample
def to_hitpick(self, submission_rsl:str) -> dict|None:
@@ -511,7 +514,7 @@ class BacterialCultureSample(BasicSample):
# rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
# rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
__mapper_args__ = {"polymorphic_identity": "bacterial_culture_sample", "polymorphic_load": "inline"}
__mapper_args__ = {"polymorphic_identity": "Bacterial Culture Sample", "polymorphic_load": "inline"}
# def to_string(self) -> str:
# """
@@ -543,10 +546,10 @@ class SubmissionSampleAssociation(Base):
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
"""
__tablename__ = "_submission_sample"
sample_id = Column(INTEGER, ForeignKey("_samples.id"), primary_key=True)
sample_id = Column(INTEGER, ForeignKey("_samples.id"), nullable=False)
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True)
row = Column(INTEGER)
column = Column(INTEGER)
row = Column(INTEGER, primary_key=True)
column = Column(INTEGER, primary_key=True)
submission = relationship(BasicSubmission, back_populates="submission_sample_associations")
@@ -569,6 +572,9 @@ class SubmissionSampleAssociation(Base):
self.row = row
self.column = column
def __repr__(self) -> str:
return f"<SubmissionSampleAssociation({self.submission.rsl_plate_num} & {self.sample.submitter_id})"
class WastewaterAssociation(SubmissionSampleAssociation):
ct_n1 = Column(FLOAT(2)) #: AKA ct for N1