class SequenceSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source="owner.username")
project__id = serializers.CharField(source='project.id')
project__title = serializers.CharField(source='project.title')
biosample__id = serializers.CharField(source='biosample.id')
biosample__ScientificName = serializers.CharField(
source='biosample.ScientificName')
seqstat__id = serializers.CharField(source='seqstat.id')
seqstat__r_Reads = serializers.IntegerField(source='seqstat.r_Reads')
seqstat__r_Yield = serializers.CharField(source='seqstat.r_Yield')
seqstat__r_GeeCee = serializers.CharField(source='seqstat.r_GeeCee')
seqstat__r_MinLen = serializers.CharField(source='seqstat.r_MinLen')
seqstat__r_AvgLen = serializers.CharField(source='seqstat.r_AvgLen')
seqstat__r_MaxLen = serializers.CharField(source='seqstat.r_MaxLen')
seqstat__r_AvgQual = serializers.CharField(source='seqstat.r_AvgQual')
seqstat__r_ErrQual = serializers.CharField(source='seqstat.r_ErrQual')
seqstat__r_Ambiguous = serializers.CharField(source='seqstat.r_Ambiguous')
seqstat__q_Reads = serializers.CharField(source='seqstat.q_Reads')
seqstat__q_Yield = serializers.CharField(source='seqstat.q_Yield')
seqstat__q_GeeCee = serializers.CharField(source='seqstat.q_GeeCee')
seqstat__q_MinLen = serializers.CharField(source='seqstat.q_MinLen')
seqstat__q_AvgLen = serializers.CharField(source='seqstat.q_AvgLen')
seqstat__q_MaxLen = serializers.CharField(source='seqstat.q_MaxLen')
seqstat__q_AvgQual = serializers.CharField(source='seqstat.q_AvgQual')
seqstat__q_ErrQual = serializers.CharField(source='seqstat.q_ErrQual')
seqstat__q_Ambiguous = serializers.CharField(source='seqstat.q_Ambiguous')
class Meta:
model = Sequence
fields = "__all__"
class AccountSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
def create(self, validated_data):
password = validated_data.pop('password', None)
instance = self.Meta.model(**validated_data)
if password is not None:
instance.set_password(password)
instance.save()
return instance
def update(self, instance, validated_data):
instance.username = validated_data.get('username', instance.username)
instance.email = validated_data.get('email', instance.email)
password = validated_data.pop('password', None)
if password is not None:
instance.set_password(password)
instance.save()
return instance
class Meta:
model = Account
fields = ('email', 'username', 'password', '_id', 'projects',
'biosamples')
extra_kwargs = {'password': {'write_only': True}}
class SeqstatSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source="owner.username")
class Meta:
model = Seqstat
fields = "__all__"
class ProjectSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source="owner.username")
#sequences = serializers.StringRelatedField(many=True)
sequences = serializers.HyperlinkedRelatedField(
many=True, read_only=True, view_name='seq:sequence-detail')
class Meta:
model = Project
fields = "__all__"
class BioSampleSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
project__id = serializers.ReadOnlyField(source='project.id')
project__title = serializers.ReadOnlyField(source='project.title')
owner = serializers.ReadOnlyField(source="owner.username")
sequences = serializers.HyperlinkedRelatedField(
many=True, read_only=True, view_name='seq:sequence-detail')
class Meta:
model = BioSample
fields = "__all__"
class StatsSerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source='owner.username')
assembly__biosample__project__id = serializers.ReadOnlyField(
source='assembly.biosample.project.id')
assembly__biosample__project__title = serializers.ReadOnlyField(
source='assembly.biosample.project.title')
biosample__id = serializers.ReadOnlyField(source='assembly.biosample.id')
assembly__biosample__sampleType = serializers.ReadOnlyField(
source='assembly.biosample.sampleType')
class Meta:
model = Stats
fields = '__all__'
read_only_fields = ['owner']
ordering = ['assembly__biosample__project__id']
class AssemblySerializer(serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source='owner.username')
# reterieve fields from the related collection
biosample__sampleType = serializers.ReadOnlyField(
source='biosample.sampleType')
biosample__ScientificName = serializers.ReadOnlyField(
source='biosample.ScientificName')
biosample__project__id = serializers.ReadOnlyField(
source='biosample.project.id')
biosample__project__title = serializers.ReadOnlyField(
source='biosample.project.title')
class Meta:
model = Assembly
fields = '__all__'
read_only_fields = ['owner']
ordering = ['biosample__project__id']
class MlstSerializer(FlattenMixin, serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source='owner.username')
assembly__biosample__project__id = serializers.ReadOnlyField(
source='assembly.biosample.project.id')
assembly__biosample__project__title = serializers.ReadOnlyField(
source='assembly.biosample.project.title')
assembly_biosample__id = serializers.ReadOnlyField(
source='assembly.biosample.id')
assembly__biosample__sampleType = serializers.ReadOnlyField(
source='assembly.biosample.sampleType')
class Meta:
model = Mlst
fields = '__all__'
ordering = ['assembly__biosample__project__id']
read_only_fields = ['owner']
flatten = ["profile"]
class ResistomeSerializer(FlattenMixin, serializers.ModelSerializer):
_id = ObjectIdField(read_only=True)
owner = serializers.ReadOnlyField(source='owner.username')
#assembly = serializers.ReadOnlyField(source='assembly.id')
# reterieve fields from the related collection
assembly__biosample__project__id = serializers.ReadOnlyField(
source='assembly.biosample.project.id')
assembly__biosample__project__title = serializers.ReadOnlyField(
source='assembly.biosample.project.title')
assembly__biosample__id = serializers.ReadOnlyField(
source='assembly.biosample.id')
assembly__biosample__sampleType = serializers.ReadOnlyField(
source='assembly.biosample.sampleType')
class Meta:
model = Resistome
ordering = ['assembly__biosample__project__id']
fields = '__all__'
read_only_fields = ['owner']
flatten = ["profile"]