class DetailedComputedFileSerializer(serializers.ModelSerializer):
result = ComputationalResultRelationSerializer(many=False, read_only=False)
samples = DetailedExperimentSampleSerializer(many=True)
compendia_organism_name = serializers.CharField(
source="compendia_organism__name", read_only=True)
class Meta:
model = ComputedFile
fields = (
"id",
"filename",
"samples",
"size_in_bytes",
"is_qn_target",
"is_smashable",
"is_qc",
"is_compendia",
"quant_sf_only",
"compendia_version",
"compendia_organism_name",
"sha1",
"s3_bucket",
"s3_key",
"s3_url",
"download_url",
"created_at",
"last_modified",
"result",
)
class DetailedExperimentSerializer(serializers.ModelSerializer):
annotations = ExperimentAnnotationSerializer(many=True, source="experimentannotation_set")
samples = DetailedExperimentSampleSerializer(many=True)
sample_metadata = serializers.ReadOnlyField(source="sample_metadata_fields")
organism_names = serializers.StringRelatedField(many=True, source="organisms", read_only=True)
class Meta:
model = Experiment
fields = (
"id",
"title",
"description",
"annotations",
"samples",
"protocol_description",
"accession_code",
"alternate_accession_code",
"source_database",
"source_url",
"has_publication",
"publication_title",
"publication_doi",
"publication_authors",
"pubmed_id",
"source_first_published",
"source_last_modified",
"submitter_institution",
"last_modified",
"created_at",
"organism_names",
"sample_metadata",
"num_total_samples",
"num_processed_samples",
"num_downloadable_samples",
)
class ComputedFileListSerializer(serializers.ModelSerializer):
result = ComputationalResultNoFilesRelationSerializer(many=False)
samples = DetailedExperimentSampleSerializer(many=True)
compendia_organism_name = serializers.CharField(
source="compendia_organism__name", read_only=True)
def __init__(self, *args, **kwargs):
super(ComputedFileListSerializer, self).__init__(*args, **kwargs)
if "context" in kwargs:
# only include the field `download_url` if a valid token is specified
# the token lookup happens in the view.
if "token" not in kwargs["context"]:
self.fields.pop("download_url")
class Meta:
model = ComputedFile
fields = (
"id",
"filename",
"samples",
"size_in_bytes",
"is_qn_target",
"is_smashable",
"is_qc",
"is_compendia",
"quant_sf_only",
"compendium_version",
"compendia_organism_name",
"sha1",
"s3_bucket",
"s3_key",
"s3_url",
"download_url",
"created_at",
"last_modified",
"result",
)
read_only_fields = fields
extra_kwargs = {
"download_url": {
"help_text":
"This will contain an url to download the file. You must send a valid [token](#tag/token) in order to receive this."
}
}
class DetailedOriginalFileSerializer(OriginalFileSerializer):
samples = DetailedExperimentSampleSerializer(many=True)
processor_jobs = ProcessorJobRelationSerializer(many=True)
downloader_jobs = DownloaderJobRelationSerializer(many=True)