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utils.py
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utils.py
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from collections import namedtuple
import dateutil.parser
from DataRepo.models import (
Animal,
Compound,
Sample,
Study,
Tissue,
value_from_choices_label,
)
class SampleTableLoader:
"""
Load a sample table
"""
SampleTableHeaders = namedtuple(
"SampleTableHeaders",
[
"SAMPLE_NAME",
"SAMPLE_DATE",
"SAMPLE_RESEARCHER",
"TISSUE_NAME",
"STUDY_NAME",
"STUDY_DESCRIPTION",
"ANIMAL_NAME",
"ANIMAL_WEIGHT",
"ANIMAL_AGE",
"ANIMAL_SEX",
"ANIMAL_GENOTYPE",
"ANIMAL_FEEDING_STATUS",
"ANIMAL_DIET",
"ANIMAL_STATE",
"TRACER_COMPOUND_NAME",
"TRACER_LABELED_ELEMENT",
"TRACER_LABELED_COUNT",
"TRACER_INFUSION_RATE",
"TRACER_INFUSION_CONCENTRATION",
],
)
DefaultSampleTableHeaders = SampleTableHeaders(
SAMPLE_NAME="SAMPLE_NAME",
SAMPLE_DATE="SAMPLE_DATE",
SAMPLE_RESEARCHER="SAMPLE_RESEARCHER",
TISSUE_NAME="TISSUE_NAME",
STUDY_NAME="STUDY_NAME",
STUDY_DESCRIPTION="STUDY_DESCRIPTION",
ANIMAL_NAME="ANIMAL_NAME",
ANIMAL_WEIGHT="ANIMAL_WEIGHT",
ANIMAL_AGE="ANIMAL_AGE",
ANIMAL_SEX="ANIMAL_SEX",
ANIMAL_GENOTYPE="ANIMAL_GENOTYPE",
ANIMAL_FEEDING_STATUS="ANIMAL_FEEDING_STATUS",
ANIMAL_DIET="ANIMAL_DIET",
ANIMAL_STATE="ANIMAL_STATE",
TRACER_COMPOUND_NAME="TRACER_COMPOUND_NAME",
TRACER_LABELED_ELEMENT="TRACER_LABELED_ELEMENT",
TRACER_LABELED_COUNT="TRACER_LABELED_COUNT",
TRACER_INFUSION_RATE="TRACER_INFUSION_RATE",
TRACER_INFUSION_CONCENTRATION="TRACER_INFUSION_CONCENTRATION",
)
def __init__(self, sample_table_headers=DefaultSampleTableHeaders):
self.headers = sample_table_headers
self.blank = ""
def load_sample_table(self, data):
for row in data:
# Skip BLANK rows
if row[self.headers.TISSUE_NAME] == self.blank:
print("Skipping row: Tissue field is empty, assuming blank sample")
continue
# Tissue
tissue, created = Tissue.objects.get_or_create(
name=row[self.headers.TISSUE_NAME]
)
if created:
print(f"Created new record: Tissue:{tissue}")
try:
tissue.full_clean()
tissue.save()
except Exception as e:
print(f"Error saving record: Tissue:{tissue}")
raise (e)
# Study
study, created = Study.objects.get_or_create(
name=row[self.headers.STUDY_NAME]
)
if created:
if self.headers.STUDY_DESCRIPTION:
study.description = row[self.headers.STUDY_DESCRIPTION]
print(f"Created new record: Study:{study}")
try:
study.full_clean()
study.save()
except Exception as e:
print(f"Error saving record: Study:{study}")
raise (e)
# Animal
animal, created = Animal.objects.get_or_create(
name=row[self.headers.ANIMAL_NAME]
)
if created:
print(f"Created new record: Animal:{animal}")
if self.headers.ANIMAL_GENOTYPE:
animal.genotype = row[self.headers.ANIMAL_GENOTYPE]
if self.headers.ANIMAL_WEIGHT:
animal.body_weight = row[self.headers.ANIMAL_WEIGHT]
if self.headers.ANIMAL_FEEDING_STATUS:
animal.feeding_status = row[self.headers.ANIMAL_FEEDING_STATUS]
if self.headers.ANIMAL_AGE:
animal.age = row[self.headers.ANIMAL_AGE]
if self.headers.ANIMAL_DIET:
animal.diet = row[self.headers.ANIMAL_DIET]
if self.headers.ANIMAL_STATE:
animal.state = row[self.headers.ANIMAL_STATE]
if self.headers.ANIMAL_SEX:
animal_sex_string = row[self.headers.ANIMAL_SEX]
if animal_sex_string in animal.SEX_CHOICES:
animal_sex = animal_sex_string
else:
animal_sex = value_from_choices_label(
animal_sex_string, animal.SEX_CHOICES
)
animal.sex = animal_sex
if self.headers.TRACER_COMPOUND_NAME:
try:
tracer_compound_name = row[self.headers.TRACER_COMPOUND_NAME]
tracer_compound = Compound.objects.get(name=tracer_compound_name)
animal.tracer_compound = tracer_compound
except Compound.DoesNotExist as e:
print(
f"ERROR: {self.headers.TRACER_COMPOUND_NAME} not found: Compound:{tracer_compound_name}"
)
raise (e)
if self.headers.TRACER_LABELED_ELEMENT:
tracer_labeled_atom = value_from_choices_label(
row[self.headers.TRACER_LABELED_ELEMENT],
animal.TRACER_LABELED_ELEMENT_CHOICES,
)
animal.tracer_labeled_atom = tracer_labeled_atom
if self.headers.TRACER_LABELED_COUNT:
animal.tracer_labeled_count = row[self.headers.TRACER_LABELED_COUNT]
if self.headers.TRACER_INFUSION_RATE:
animal.tracer_infusion_rate = row[self.headers.TRACER_INFUSION_RATE]
if self.headers.TRACER_INFUSION_CONCENTRATION:
animal.tracer_infusion_concentration = row[
self.headers.TRACER_INFUSION_CONCENTRATION
]
try:
animal.full_clean()
animal.save()
except Exception as e:
print(f"Error saving record: Animal:{animal}")
raise (e)
# Sample
sample_name = row[self.headers.SAMPLE_NAME]
try:
sample = Sample.objects.get(name=sample_name)
except Sample.DoesNotExist:
print(f"Creating new record: Sample:{sample_name}")
sample = Sample(
name=row[self.headers.SAMPLE_NAME],
researcher=row[self.headers.SAMPLE_RESEARCHER],
animal=animal,
tissue=tissue,
)
if self.headers.SAMPLE_DATE:
sample_date_str = row[self.headers.SAMPLE_DATE]
sample_date = dateutil.parser.parse(sample_date_str)
sample.date = sample_date
try:
sample.full_clean()
sample.save()
except Exception as e:
print(f"Error saving record: Sample:{sample}")
raise (e)