class ChangeSerializer(ShareModelSerializer):
self = serializers.HyperlinkedIdentityField(view_name='api:change-detail')
target_type = serializers.StringRelatedField()
class Meta:
model = models.Change
fields = ('self', 'id', 'change', 'node_id', 'type', 'target_type', 'target_id')
class DemographicDataSerializer(UuidHyperlinkedModelSerializer):
resource_name = "demographics"
country = serializers.CharField(default="")
date_created = serializers.DateTimeField(read_only=True,
source="created_at")
url = serializers.HyperlinkedIdentityField(
view_name="api:demographicdata-detail", lookup_field="uuid")
class Meta:
model = DemographicData
fields = (
"url",
"number_of_children",
"child_birthdays",
"languages_spoken_at_home",
"number_of_guardians",
"number_of_guardians_explanation",
"race_identification",
"age",
"gender",
"education_level",
"spouse_education_level",
"annual_income",
"former_lookit_annual_income",
"lookit_referrer",
"number_of_books",
"additional_comments",
"country",
"state",
"density",
"extra",
"date_created",
"pk",
)
class StudySerializer(UuidHyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(view_name="api:study-detail",
lookup_field="uuid")
responses = PatchedHyperlinkedRelatedField(
queryset=Response.objects,
many=True,
related_link_view_name="api:study-responses-list",
related_link_url_kwarg="study_uuid",
related_link_lookup_field="uuid",
)
class Meta:
model = Study
fields = (
"url",
"name",
# "date_modified",
"short_description",
"long_description",
"criteria",
"duration",
"contact_info",
"image",
"structure",
"generator",
"use_generator",
"display_full_screen",
"exit_url",
"state",
"public",
# "organization",
# "creator",
"responses",
"pk",
)
class ProjectSerializer(BaseModelSerializer):
events = serializers.HyperlinkedIdentityField(many=True,
view_name='event-detail')
class Meta:
model = Project
fields = '__all__'
class ChildSerializer(UuidHyperlinkedModelSerializer):
lookup_field = "uuid"
url = serializers.HyperlinkedIdentityField(view_name="api:child-detail",
lookup_field="uuid")
user = PatchedHyperlinkedRelatedField(
queryset=User.objects,
related_link_view_name="api:user-detail",
related_link_lookup_field="user.uuid",
related_link_url_kwarg="uuid",
)
class Meta:
model = Child
fields = (
"url",
"user",
"given_name",
"birthday",
"gender",
"age_at_birth",
"additional_information",
"deleted",
"former_lookit_profile_id",
"pk",
)
class PageHeaderSerializer(serializers.ModelSerializer):
class Meta:
model = PageHeader
exclude = ('id', )
image = serializers.HyperlinkedIdentityField(read_only=True,
view_name='image-detail')
class ResponseSerializer(UuidHyperlinkedModelSerializer):
"""Gets hyperlink related fields.
XXX: It's important to keep read_only set to true here - otherwise, a queryset is necessitated, which implicates
get_attribute from ResourceRelatedField
"""
created_on = serializers.DateTimeField(read_only=True,
source="date_created")
url = serializers.HyperlinkedIdentityField(view_name="api:response-detail",
lookup_field="uuid")
study = PatchedHyperlinkedRelatedField(
read_only=True,
related_link_view_name="api:study-detail",
related_link_lookup_field="study.uuid",
related_link_url_kwarg="uuid",
)
user = PatchedHyperlinkedRelatedField(
read_only=True,
source="child",
related_link_view_name="api:user-detail",
related_link_lookup_field="child.user.uuid",
related_link_url_kwarg="uuid",
required=False,
)
child = PatchedHyperlinkedRelatedField(
read_only=True,
related_link_view_name="api:child-detail",
related_link_lookup_field="child.uuid",
related_link_url_kwarg="uuid",
)
demographic_snapshot = PatchedHyperlinkedRelatedField(
read_only=True,
related_link_view_name="api:demographicdata-detail",
related_link_lookup_field="demographic_snapshot.uuid",
related_link_url_kwarg="uuid",
required=False,
)
class Meta:
model = Response
fields = (
"url",
"conditions",
"global_event_timings",
"exp_data",
"sequence",
"completed",
"child",
"user",
"study",
"completed_consent_frame",
"demographic_snapshot",
"created_on",
"is_preview",
"pk",
"withdrawn",
)
class OrganizationSerializer(UuidHyperlinkedModelSerializer):
resource_name = "organizations"
url = serializers.HyperlinkedIdentityField(view_name="organization-detail",
lookup_field="uuid")
class Meta:
model = Organization
fields = ("name", "url", "pk")
class AntiSmashGeneClusterSerializer(m_serializers.DocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:antismash-gene-clusters-detail',
lookup_field='accession',
)
class Meta:
model = m_models.AntiSmashGeneCluster
fields = '__all__'
class GenomePropertySerializer(m_serializers.DocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:genome-properties-detail',
lookup_field='accession',
)
class Meta:
model = m_models.GenomeProperty
fields = '__all__'
class KeggOrthologSerializer(m_serializers.DocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:kegg-orthologs-detail',
lookup_field='accession',
)
class Meta:
model = m_models.KeggOrtholog
fields = '__all__'
class PfamSerializer(m_serializers.DocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:pfam-detail',
lookup_field='accession',
)
class Meta:
model = m_models.PfamEntry
fields = '__all__'
class GoTermRetriveSerializer(m_serializers.DynamicDocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:goterms-detail',
lookup_field='accession',
)
count = serializers.IntegerField(required=False)
class Meta:
model = m_models.GoTerm
fields = '__all__'
class KeggOrthologRetrieveSerializer(m_serializers.DynamicDocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:kegg-orthologs-detail',
lookup_field='accession',
)
count = serializers.IntegerField(required=True)
class Meta:
model = m_models.KeggOrtholog
fields = '__all__'
class InterproIdentifierSerializer(m_serializers.DocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:interproidentifier-detail',
lookup_field='accession',
)
def get_analysis(self, obj):
return None
class Meta:
model = m_models.InterproIdentifier
fields = '__all__'
class BasicUserSerializer(UuidHyperlinkedModelSerializer):
resource_name = "users"
url = serializers.HyperlinkedIdentityField(view_name="user-detail",
lookup_field="uuid")
demographics = PatchedHyperlinkedRelatedField(
queryset=DemographicData.objects,
many=True,
related_link_view_name="user-demographics-list",
related_link_url_kwarg="user_uuid",
related_link_lookup_field="uuid",
)
organization = PatchedHyperlinkedRelatedField(
queryset=Organization.objects,
related_link_view_name="organization-detail",
related_link_lookup_field="organization.uuid",
related_link_url_kwarg="uuid",
)
children = PatchedHyperlinkedRelatedField(
queryset=Child.objects,
many=True,
related_link_view_name="user-children-list",
related_link_url_kwarg="user_uuid",
related_link_lookup_field="uuid",
)
class Meta:
model = User
fields = (
"url",
"given_name",
"middle_name",
"family_name",
"nickname",
"identicon",
"is_active",
"is_staff",
"is_researcher",
"demographics",
"organization",
"children",
"former_lookit_id",
"linked_former_lookit_ids",
"email_next_session",
"email_new_studies",
"email_study_updates",
"email_response_questions",
"date_created",
"pk",
)
class AntiSmashGeneClusterRetrieveSerializer(
m_serializers.DynamicDocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:antismash-gene-clusters-detail',
lookup_field='accession',
)
count = serializers.IntegerField(required=True)
class Meta:
model = m_models.AntiSmashGeneCluster
fields = '__all__'
class GenomePropertyRetrieveSerializer(m_serializers.DynamicDocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:genome-properties-detail',
lookup_field='accession',
)
presence = serializers.CharField(source="get_presence_display",
required=True)
class Meta:
model = m_models.GenomeProperty
fields = '__all__'
class KeggModuleRetrieveSerializer(m_serializers.DynamicDocumentSerializer,
serializers.HyperlinkedModelSerializer):
url = serializers.HyperlinkedIdentityField(
view_name='emgapi_v1:keggmodules-detail',
lookup_field='accession',
)
completeness = serializers.FloatField(required=True)
matching_kos = serializers.ListField()
missing_kos = serializers.ListField()
class Meta:
model = m_models.KeggModule
fields = '__all__'
class ChangeSetSerializer(ShareModelSerializer):
# changes = ChangeSerializer(many=True)
change_count = serializers.SerializerMethodField()
self = serializers.HyperlinkedIdentityField(view_name='api:changeset-detail')
source = ShareUserSerializer(source='normalized_data.source')
status = serializers.SerializerMethodField()
def get_status(self, obj):
return ChangeSet.STATUS[obj.status]
def get_change_count(self, obj):
return obj.changes.count()
class Meta:
model = models.ChangeSet
fields = ('self', 'id', 'submitted_at', 'change_count', 'source', 'status')
class ResponseSerializer(UUIDSerializerMixin, ModelSerializer):
created_on = serializers.DateTimeField(read_only=True,
source='date_created')
url = serializers.HyperlinkedIdentityField(view_name='response-detail',
lookup_field='uuid')
study = UUIDResourceRelatedField(
queryset=Study.objects,
many=False,
related_link_view_name='study-detail',
related_link_lookup_field='uuid',
)
user = UUIDResourceRelatedField(source='child.user',
queryset=User.objects,
many=False,
related_link_view_name='user-list',
related_link_lookup_field='uuid',
required=False)
child = UUIDResourceRelatedField(
queryset=Child.objects,
many=False,
related_link_view_name='child-detail',
related_link_lookup_field='uuid',
)
demographic_snapshot = UUIDResourceRelatedField(
queryset=DemographicData.objects,
many=False,
related_link_view_name='demographicdata-detail',
related_link_lookup_field='uuid',
required=False)
class Meta:
model = Response
fields = (
'url',
'conditions',
'global_event_timings',
'exp_data',
'sequence',
'completed',
'child',
'user',
'study',
'demographic_snapshot',
'created_on',
'pk',
)
class LabSerializer(UuidHyperlinkedModelSerializer):
resource_name = "labs"
url = serializers.HyperlinkedIdentityField(view_name="api:lab-detail",
lookup_field="uuid")
class Meta:
model = Lab
fields = (
"name",
"institution",
"principal_investigator_name",
"lab_website",
"description",
"approved_to_test",
"url",
"pk",
)
class StudySerializer(UUIDSerializerMixin, ModelSerializer):
url = serializers.HyperlinkedIdentityField(view_name='study-detail',
lookup_field='uuid')
organization = UUIDResourceRelatedField(
queryset=Organization.objects,
related_link_view_name='organization-detail',
related_link_lookup_field='uuid',
many=False)
creator = UUIDResourceRelatedField(queryset=User.objects,
related_link_view_name='user-detail',
related_link_lookup_field='uuid',
many=False)
responses = UUIDResourceRelatedField(
queryset=Response.objects,
many=True,
related_link_view_name='study-responses-list',
related_link_url_kwarg='study_uuid',
related_link_lookup_field='uuid',
)
class Meta:
model = Study
fields = (
'url',
'name',
'date_modified',
'short_description',
'long_description',
'criteria',
'duration',
'contact_info',
'image',
'structure',
'display_full_screen',
'exit_url',
'state',
'public',
'organization',
'creator',
'responses',
'pk',
)
class ResponseWriteableSerializer(UuidResourceModelSerializer):
"""Serialize according to the way the frontend likes to send data - true-ID specific."""
url = serializers.HyperlinkedIdentityField(view_name="api:response-detail",
lookup_field="uuid")
study = PatchedResourceRelatedField(
queryset=Study.objects,
related_link_view_name="api:study-detail",
related_link_lookup_field="study_id",
related_link_url_kwarg="uuid",
)
child = PatchedResourceRelatedField(
queryset=Child.objects,
related_link_view_name="api:child-detail",
related_link_lookup_field="child_id",
related_link_url_kwarg="uuid",
)
def create(self, validated_data):
"""Implicitly capture Demographic Data."""
validated_data["demographic_snapshot_id"] = validated_data.get(
"child").user.latest_demographics.id
return super().create(validated_data)
class Meta:
model = Response
fields = (
"url",
"conditions",
"global_event_timings",
"exp_data",
"sequence",
"completed",
"child",
"study",
"completed_consent_frame",
"is_preview",
"pk",
"withdrawn",
)
class FloipListSerializer(serializers.HyperlinkedModelSerializer):
"""
FloipListSerializer class.
"""
url = serializers.HyperlinkedIdentityField(view_name='flow-results-detail',
lookup_field='uuid')
id = ReadOnlyUUIDField(source='uuid') # pylint: disable=C0103
name = serializers.ReadOnlyField(source='id_string')
created = serializers.ReadOnlyField(source='date_created')
modified = serializers.ReadOnlyField(source='date_modified')
class JSONAPIMeta: # pylint: disable=old-style-class,no-init,R0903
"""
JSON API metaclass.
"""
resource_name = 'packages'
class Meta:
model = XForm
fields = ('url', 'id', 'name', 'title', 'created', 'modified')
class FeedbackSerializer(UUIDSerializerMixin, ModelSerializer):
url = serializers.HyperlinkedIdentityField(view_name='feedback-detail',
lookup_field='uuid')
response = UUIDResourceRelatedField(
queryset=Response.objects,
many=False,
related_link_view_name='response-detail',
related_link_lookup_field='uuid',
)
researcher = UUIDResourceRelatedField(
read_only=True,
many=False,
related_link_view_name='user-detail',
related_link_lookup_field='uuid',
)
class Meta:
model = Feedback
fields = ('url', 'comment', 'response', 'researcher')
read_only_fields = ('researcher', )
class FeedbackSerializer(UuidResourceModelSerializer):
url = serializers.HyperlinkedIdentityField(view_name="api:feedback-detail",
lookup_field="uuid")
response = PatchedResourceRelatedField(
queryset=Response.related_manager,
related_link_view_name="api:response-detail",
related_link_lookup_field="response.uuid",
related_link_url_kwarg="uuid",
)
researcher = PatchedResourceRelatedField(
read_only=True,
related_link_view_name="api:user-detail",
related_link_lookup_field="researcher.uuid",
related_link_url_kwarg="uuid",
)
class Meta:
model = Feedback
fields = ("url", "comment", "response", "researcher")
read_only_fields = ("researcher", )
class FloipSerializer(serializers.HyperlinkedModelSerializer):
"""
FloipSerializer class.
"""
url = serializers.HyperlinkedIdentityField(view_name='floip-detail',
lookup_field='pk')
profile = serializers.SerializerMethodField()
created = serializers.ReadOnlyField(source='date_created')
modified = serializers.ReadOnlyField(source='date_modified')
# pylint: disable=invalid-name
flow_results_specification_version = serializers.SerializerMethodField()
resources = serializers.SerializerMethodField()
class JSONAPIMeta: # pylint: disable=old-style-class,no-init,R0903
"""
JSON API metaclass.
"""
resource_name = 'packages'
class Meta:
model = XForm
fields = ('url', 'id', 'id_string', 'title', 'profile', 'created',
'modified', 'flow_results_specification_version',
'resources')
def get_profile(self, value): # pylint: disable=no-self-use,W0613
"""
Returns the data-package profile.
"""
return 'data-package'
# pylint: disable=no-self-use,unused-argument
def get_flow_results_specification_version(self, value):
"""
Returns the flow results specification version.
"""
return '1.0.0-rc1'
def get_resources(self, value): # pylint: disable=no-self-use,W0613
"""
Returns empty dict, a dummy holder for the eventually generated data
package resources.
"""
return {}
def _process_request(self, request, update_instance=None):
data = deepcopy(request.data)
if 'profile' in data and data['profile'] == 'flow-results-package':
data['profile'] = 'data-package'
descriptor = BytesIO(json.dumps(data).encode('utf-8'))
descriptor.seek(0, os.SEEK_END)
floip_file = InMemoryUploadedFile(descriptor,
'floip_file',
request.data.get('name') + '.json',
'application/json',
descriptor.tell(),
charset=None)
kwargs = {
'user': request.user,
'post': None,
'files': {
'floip_file': floip_file
},
'owner': request.user,
}
if update_instance:
kwargs['id_string'] = update_instance.id_string
kwargs['project'] = update_instance.project
instance = do_publish_xlsform(**kwargs)
if isinstance(instance, XForm):
return instance
raise serializers.ValidationError(instance)
def create(self, validated_data):
request = self.context['request']
return self._process_request(request)
def update(self, instance, validated_data):
request = self.context['request']
return self._process_request(request, instance)
def to_representation(self, instance):
request = self.context['request']
data_id = str(UUID(instance.uuid))
data_url = request.build_absolute_uri(
reverse('flow-results-responses', kwargs={'uuid': data_id}))
package = survey_to_floip_package(json.loads(instance.json), data_id,
instance.date_created,
instance.date_modified, data_url)
data = package.descriptor
if data['profile'] != 'flow-results-package':
data['profile'] = 'flow-results-package'
return data
class RoomNodeInstallationSerializer(serializers.HyperlinkedModelSerializer):
included_serializers = {
"node": "core.serializers.NodeSerializer",
"room": "core.serializers.RoomSerializer",
# "timeseries": "core.serializers.TimeseriesSerializer",
}
node = ResourceRelatedField(
queryset=Node.objects.all(),
related_link_url_kwarg="installation_pk",
related_link_view_name="installation-related-node",
)
room = ResourceRelatedField(
queryset=Room.objects.all(), related_link_view_name="installation-related"
)
to_timestamp_s = serializers.IntegerField(required=False)
# Image of the installation (optional). Handle upload in a separate serializer.
image = serializers.ImageField(required=False, read_only=True)
# Additional fields to merge the node installation with its samples.
timeseries = serializers.ListField(child=SimpleSampleSerializer(), read_only=True)
query_timestamp_s = serializers.IntegerField(read_only=True)
sample_count = serializers.IntegerField(read_only=True)
url = serializers.HyperlinkedIdentityField(view_name="installation-detail")
class Meta:
model = RoomNodeInstallation
fields = [
"room",
"node",
"timeseries",
"query_timestamp_s",
"from_timestamp_s",
"to_timestamp_s",
"sample_count",
"description",
"image",
"is_public",
"url",
]
def __init__(self, *args, **kwargs):
# Don't pass the "include_timeseries" arg up to the superclass
include_timeseries = kwargs.pop("include_timeseries", None)
# Instantiate the superclass normally
super().__init__(*args, **kwargs)
if not include_timeseries:
self.fields.pop("timeseries")
def get_owner(self):
"""Return the owner of the resource, once data is validated."""
room = self.validated_data["room"]
site = room.site
owner = site.operator
return owner
def validate(self, attrs):
"""
Ensure that the node is owned by the same organization as the room.
"""
logger.debug(
"For a new or updated installation, validate that node and room belong to the same owner."
)
try:
room = attrs["room"]
node = attrs["node"]
except KeyError:
raise serializers.ValidationError(
"Both the Room reference and the node reference must be provided."
)
if room.site.operator != node.owner:
raise serializers.ValidationError(
"In an installation, Node and room must belong to the same owner."
)
return attrs
class ProjectSerializer(serializers.ModelSerializer):
obj_url = serializers.HyperlinkedIdentityField(view_name='any')
class Meta:
model = test_models.Project
fields = ('id', 'obj_url')
