6👍
You can do it like below
class SpeciesSerializer(serializers.HyperlinkedModelSerializer):
class Meta:
model = Species
fields = (
'url', 'id', 'canonical_name', 'slug', 'species', 'genus',
'subfamily', 'family', 'order','class', 'phylum',
'ncbi_id', 'ncbi_taxonomy',
)
read_only_fields = ('slug',)
extra_kwargs = {
'url': {'lookup_field': 'slug'}
}
SpeciesSerializer._declared_fields["class"] = serializers.CharField(source="class_name")
As explained in below answer
19👍
You can rename field in the overloaded version of get_fields()
method
class MySerializer(serializers.Serializer):
class_ = serializers.ReadOnlyField()
def get_fields(self):
result = super().get_fields()
# Rename `class_` to `class`
class_ = result.pop('class_')
result['class'] = class_
return result
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15👍
You can set the property of a class via strings as such:
class SpeciesSerializer(serializers.Serializer):
species = serializers.CharField()
genus = serializers.CharField()
family = serializers.CharField()
vars()['class'] = serializers.CharField()
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5👍
Other software developers in the field of Bioinformatics might be interested in a solution of this problem, so I post here my approach as suggested by Alasdair.
The goal is to create a model for a living species, for the sake of simplicity let’s say an animal, and create an endpoint with Django REST Framework representing the correct taxonomic ranks.
models.py
from django.db import models
class Animal(models.Model):
canonical_name = models.CharField(max_length=100, unique=True)
species = models.CharField(max_length=60, unique=True)
genus = models.CharField(max_length=30)
family = models.CharField(max_length=30)
order = models.CharField(max_length=30)
# we can't use class as field name
class_name = models.CharField('Class', db_column='class', max_length=30)
phylum = models.CharField(max_length=30)
# we don't need to define kingdom and domain
# it's clear that it is an animal and eukaryote
def __str__(self):
return '{} ({})'.format(self.canonical_name, self.species)
serializers.py
from collections import OrderedDict
from rest_framework import serializers
from .models import Species
class SpeciesSerializer(serializers.HyperlinkedModelSerializer):
class Meta:
model = Animal
fields = ('url', 'id', 'canonical_name', 'species', 'genus',
'subfamily', 'family', 'order', 'class_name', 'phylum')
def to_representation(self, obj):
# call the parent method and get an OrderedDict
data = super(SpeciesSerializer, self).to_representation(obj)
# generate a list of the keys and replace the key 'class_name'
keys = list(data.keys())
keys.insert(keys.index('class_name'), 'class')
keys.remove('class_name')
# remove 'class_name' and assign its value to a new key 'class'
class_name = data.pop('class_name')
data.update({'class': class_name})
# create new OrderedDict with the order given by the keys
response = OrderedDict((k, data[k]) for k in keys)
return response
The method to_representation
helps us to manipulate the output. I have put some extra work here to get the taxonomic ranks in the desired order.
Thus for the red fox the output looks like this:
Red fox (Vulpes vulpes)
{
"url": "http://localhost:8000/animal/1",
"id": 1,
"canonical_name": "Red fox",
"species": "Vulpes vulpes",
"genus": "Vulpes",
"family": "Canidae",
"order": "Carnivora",
"class": "Mammalia",
"phylum": "Chordata"
}
It is a simplified example and in reality you’d have many more fields or possibly a model for every taxonomic rank, but somewhere you might come across the conflict between the reserved word class
and the taxonomic rank class.
I hope this can help other people too.
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