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

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This commit is contained in:
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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61
src/submissions/backend/db/models/submissions.py
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@@ -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"}