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Addition of WW artic parsers, large-scale shake-up of parser structure.

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Landon Wark
2023-06-08 14:43:36 -05:00
parent 1d6823705c
commit a7132cd1b4
14 changed files with 376 additions and 56 deletions
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2
src/submissions/backend/db/models/__init__.py
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@@ -10,4 +10,4 @@ from .controls import Control, ControlType
from .kits import KitType, ReagentType, Reagent, Discount
from .organizations import Organization, Contact
from .samples import WWSample, BCSample
from .submissions import BasicSubmission, BacterialCulture, Wastewater
from .submissions import BasicSubmission, BacterialCulture, Wastewater, WastewaterArtic

40
src/submissions/backend/db/models/samples.py
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@@ -37,6 +37,8 @@ class WWSample(Base):
sample_type = Column(String(8))
pcr_results = Column(JSON)
elution_well = Column(String(8)) #: location on 96 well plate
artic_rsl_plate = relationship("WastewaterArtic", back_populates="samples")
artic_well_number = Column(String(8))
def to_string(self) -> str:
@@ -131,3 +133,41 @@ class BCSample(Base):
"well": self.well_number,
"name": f"{self.sample_id} - ({self.organism})",
}
# class ArticSample(Base):
# """
# base of artic sample
# """
# __tablename__ = "_artic_samples"
# id = Column(INTEGER, primary_key=True) #: primary key
# well_number = Column(String(8)) #: location on parent plate
# rsl_plate = relationship("WastewaterArtic", back_populates="samples") #: relationship to parent plate
# rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWA_submission_id"))
# ww_sample_full_id = Column(String(64), nullable=False)
# lims_sample_id = Column(String(64), nullable=False)
# ct_1 = Column(FLOAT(2)) #: first ct value in column
# ct_2 = Column(FLOAT(2)) #: second ct value in column
# def to_string(self) -> str:
# """
# string representing sample object
# Returns:
# str: string representing location and sample id
# """
# return f"{self.well_number}: {self.ww_sample_full_id}"
# def to_sub_dict(self) -> dict:
# """
# gui friendly dictionary
# Returns:
# dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
# """
# return {
# "well": self.well_number,
# "name": self.ww_sample_full_id,
# }

61
src/submissions/backend/db/models/submissions.py
View File

@@ -161,7 +161,16 @@ class BasicSubmission(Base):
}
return output
def calculate_base_cost(self):
try:
cols_count_96 = ceil(int(self.sample_count) / 8)
except Exception as e:
logger.error(f"Column count error: {e}")
# cols_count_24 = ceil(int(self.sample_count) / 3)
try:
self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
except Exception as e:
logger.error(f"Calculation error: {e}")
# Below are the custom submission types
@@ -185,16 +194,16 @@ class BacterialCulture(BasicSubmission):
return output
def calculate_base_cost(self):
try:
cols_count_96 = ceil(int(self.sample_count) / 8)
except Exception as e:
logger.error(f"Column count error: {e}")
# cols_count_24 = ceil(int(self.sample_count) / 3)
try:
self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
except Exception as e:
logger.error(f"Calculation error: {e}")
# def calculate_base_cost(self):
# try:
# cols_count_96 = ceil(int(self.sample_count) / 8)
# except Exception as e:
# logger.error(f"Column count error: {e}")
# # cols_count_24 = ceil(int(self.sample_count) / 3)
# try:
# self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
# except Exception as e:
# logger.error(f"Calculation error: {e}")
class Wastewater(BasicSubmission):
@@ -220,14 +229,22 @@ class Wastewater(BasicSubmission):
pass
return output
def calculate_base_cost(self):
try:
cols_count_96 = ceil(int(self.sample_count) / 8) + 1 #: Adding in one column to account for 24 samples + ext negatives
except Exception as e:
logger.error(f"Column count error: {e}")
# cols_count_24 = ceil(int(self.sample_count) / 3)
try:
self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
except Exception as e:
logger.error(f"Calculation error: {e}")
# def calculate_base_cost(self):
# try:
# cols_count_96 = ceil(int(self.sample_count) / 8) + 1 #: Adding in one column to account for 24 samples + ext negatives
# except Exception as e:
# logger.error(f"Column count error: {e}")
# # cols_count_24 = ceil(int(self.sample_count) / 3)
# try:
# self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
# except Exception as e:
# logger.error(f"Calculation error: {e}")
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
"""
samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
# Can in use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
__mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}