class OutcomeSchema(BaseSchema):
participant_id = field_for(Outcome,
'participant_id',
required=True,
load_only=True,
example='PT_DZB048J5')
age_at_event_days = field_for(Outcome,
'age_at_event_days',
validate=validate_age,
example=232)
vital_status = field_for(
Outcome,
'vital_status',
validate=enum_validation_generator(VITAL_STATUS_ENUM))
disease_related = field_for(
Outcome,
'disease_related',
validate=enum_validation_generator(DISEASE_RELATED_ENUM))
class Meta(BaseSchema.Meta):
model = Outcome
resource_url = 'api.outcomes'
collection_url = 'api.outcomes_list'
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'participant':
ma.URLFor('api.participants', kf_id='<participant_id>')
})
class BiospecimenDiagnosisSchema(BaseSchema):
biospecimen_id = field_for(BiospecimenDiagnosis,
'biospecimen_id',
required=True,
load_only=True,
example='BS_ABC2C104')
diagnosis_id = field_for(BiospecimenDiagnosis,
'diagnosis_id',
required=True,
load_only=True,
example='GF_ABB2C104')
class Meta(BaseSchema.Meta):
model = BiospecimenDiagnosis
resource_url = 'api.biospecimen_diagnoses'
collection_url = 'api.biospecimen_diagnoses_list'
exclude = BaseSchema.Meta.exclude + ('biospecimen', 'diagnosis')
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'biospecimen':
ma.URLFor('api.biospecimens', kf_id='<biospecimen_id>'),
'diagnosis':
ma.URLFor('api.diagnoses', kf_id='<diagnosis_id>')
})
class CavaticaTaskSchema(BaseSchema):
cavatica_app_id = field_for(CavaticaTask,
'cavatica_app_id',
load_only=True,
required=False,
example='CA_ABB2C104')
class Meta(BaseSchema.Meta):
model = CavaticaTask
resource_url = 'api.cavatica_tasks'
collection_url = 'api.cavatica_tasks_list'
exclude = (BaseSchema.Meta.exclude + ('cavatica_app', ) +
('cavatica_task_genomic_files', ))
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'cavatica_app':
PatchedURLFor('api.cavatica_apps', kf_id='<cavatica_app_id>'),
'cavatica_task_genomic_files':
ma.URLFor('api.cavatica_task_genomic_files_list',
cavatica_task_id='<kf_id>')
})
class FamilyRelationshipSchema(BaseSchema):
participant1_id = field_for(FamilyRelationship,
'participant1_id',
required=True,
load_only=True,
example='PT_B048J5')
participant2_id = field_for(FamilyRelationship,
'participant2_id',
required=True,
load_only=True,
example='PT_B048J6')
class Meta(BaseSchema.Meta):
model = FamilyRelationship
resource_url = 'api.family_relationships'
collection_url = 'api.family_relationships_list'
exclude = BaseSchema.Meta.exclude + ('participant2', 'participant1')
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'participant1':
ma.URLFor('api.participants', kf_id='<participant1_id>'),
'participant2':
ma.URLFor('api.participants', kf_id='<participant2_id>')
})
class BiospecimenGenomicFileSchema(BaseSchema):
biospecimen_id = field_for(BiospecimenGenomicFile,
'biospecimen_id',
required=True,
load_only=True,
example='BS_ABC2C104')
genomic_file_id = field_for(BiospecimenGenomicFile,
'genomic_file_id',
required=True,
load_only=True,
example='GF_ABB2C104')
class Meta(BaseSchema.Meta):
model = BiospecimenGenomicFile
resource_url = 'api.biospecimen_genomic_files'
collection_url = 'api.biospecimen_genomic_files_list'
exclude = BaseSchema.Meta.exclude + ('biospecimen', 'genomic_file')
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'biospecimen':
ma.URLFor('api.biospecimens', kf_id='<biospecimen_id>'),
'genomic_file':
ma.URLFor('api.genomic_files', kf_id='<genomic_file_id>')
})
class CavaticaTaskGenomicFileSchema(BaseSchema):
cavatica_task_id = field_for(CavaticaTaskGenomicFile,
'cavatica_task_id',
required=True,
load_only=True,
example='CT_ABB2C104')
genomic_file_id = field_for(CavaticaTaskGenomicFile,
'genomic_file_id',
required=True,
load_only=True,
example='GF_ABB2C104')
class Meta(BaseSchema.Meta):
model = CavaticaTaskGenomicFile
resource_url = 'api.cavatica_task_genomic_files'
collection_url = 'api.cavatica_task_genomic_files_list'
exclude = BaseSchema.Meta.exclude + ('cavatica_task', 'genomic_file')
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'cavatica_task':
ma.URLFor('api.cavatica_tasks', kf_id='<cavatica_task_id>'),
'genomic_file':
ma.URLFor('api.genomic_files', kf_id='<genomic_file_id>')
})
class SequencingExperimentGenomicFileSchema(BaseSchema):
sequencing_experiment_id = field_for(SequencingExperimentGenomicFile,
'sequencing_experiment_id',
required=True,
load_only=True,
example='SE_ABB2C104')
genomic_file_id = field_for(SequencingExperimentGenomicFile,
'genomic_file_id',
required=True,
load_only=True,
example='GF_ABB2C104')
class Meta(BaseSchema.Meta):
model = SequencingExperimentGenomicFile
resource_url = 'api.sequencing_experiment_genomic_files'
collection_url = 'api.sequencing_experiment_genomic_files_list'
exclude = BaseSchema.Meta.exclude + ('sequencing_experiment',
'genomic_file')
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'sequencing_experiment':
ma.URLFor('api.sequencing_experiments',
kf_id='<sequencing_experiment_id>'),
'genomic_file':
ma.URLFor('api.genomic_files', kf_id='<genomic_file_id>')
})
class DiagnosisSchema(BaseSchema):
participant_id = field_for(Diagnosis,
'participant_id',
required=True,
load_only=True,
example='PT_DZB048J5')
age_at_event_days = field_for(Diagnosis,
'age_at_event_days',
validate=validate_age,
example=232)
diagnosis_category = field_for(
Diagnosis,
'diagnosis_category',
validate=enum_validation_generator(DIAGNOSIS_CATEGORY_ENUM))
class Meta(BaseSchema.Meta):
model = Diagnosis
resource_url = 'api.diagnoses'
collection_url = 'api.diagnoses_list'
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'participant':
ma.URLFor('api.participants', kf_id='<participant_id>'),
'biospecimen_diagnoses':
ma.URLFor('api.biospecimen_diagnoses_list', diagnosis_id='<kf_id>'),
'biospecimens':
ma.URLFor('api.biospecimens_list', diagnosis_id='<kf_id>')
})
class StudyFileSchema(BaseSchema, IndexdFileSchema):
availability = field_for(
StudyFile,
'availability',
validate=enum_validation_generator(AVAILABILITY_ENUM))
class Meta(BaseSchema.Meta):
model = StudyFile
resource_url = 'api.study_files'
collection_url = 'api.study_files_list'
study_id = field_for(StudyFile, 'study_id', required=True, load_only=True)
latest_did = field_for(StudyFile,
'latest_did',
required=False,
dump_only=True)
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'study':
ma.URLFor('api.studies', kf_id='<study_id>')
})
class GenomicFileSchema(BaseSchema, IndexdFileSchema):
class Meta(BaseSchema.Meta, IndexdFileSchema.Meta):
model = GenomicFile
resource_url = 'api.genomic_files'
collection_url = 'api.genomic_files_list'
exclude = (BaseSchema.Meta.exclude + (
'biospecimen',
'sequencing_experiment',
) + (
'task_genomic_files',
'biospecimen_genomic_files',
) + ('sequencing_experiment_genomic_files',
'read_group_genomic_files'))
paired_end = field_for(GenomicFile,
'paired_end',
validate=enum_validation_generator(PAIRED_END_ENUM))
data_type = field_for(GenomicFile,
'data_type',
validate=enum_validation_generator(DATA_TYPE_ENUM))
availability = field_for(
GenomicFile,
'availability',
validate=enum_validation_generator(AVAILABILITY_ENUM))
latest_did = field_for(GenomicFile,
'latest_did',
required=False,
dump_only=True)
_links = ma.Hyperlinks(
{
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'task_genomic_files':
ma.URLFor('api.task_genomic_files_list',
genomic_file_id='<kf_id>'),
'biospecimen_genomic_files':
ma.URLFor('api.biospecimen_genomic_files_list',
genomic_file_id='<kf_id>'),
'read_group_genomic_files':
ma.URLFor('api.read_group_genomic_files_list',
genomic_file_id='<kf_id>'),
'sequencing_experiment_genomic_files':
ma.URLFor('api.sequencing_experiment_genomic_files_list',
genomic_file_id='<kf_id>'),
'read_groups':
ma.URLFor('api.read_groups_list', genomic_file_id='<kf_id>'),
'sequencing_experiments':
ma.URLFor('api.sequencing_experiments_list',
genomic_file_id='<kf_id>'),
'biospecimens':
ma.URLFor('api.biospecimens_list', genomic_file_id='<kf_id>')
},
description='Resource links and pagination')
class InvestigatorSchema(BaseSchema):
class Meta(BaseSchema.Meta):
model = Investigator
resource_url = 'api.investigators'
collection_url = 'api.investigators_list'
exclude = BaseSchema.Meta.exclude + ('studies', )
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'studies': ma.URLFor('api.studies_list', investigator_id='<kf_id>')
})
class ParticipantSchema(BaseSchema):
study_id = field_for(Participant, 'study_id', required=True,
load_only=True)
family_id = field_for(Participant, 'family_id',
load_only=True,
required=False, example='FM_ABB2C104')
gender = field_for(Participant, 'gender',
validate=enum_validation_generator(
GENDER_ENUM))
ethnicity = field_for(Participant, 'ethnicity',
validate=enum_validation_generator(
ETHNICITY_ENUM))
race = field_for(Participant, 'race',
validate=enum_validation_generator(
RACE_ENUM))
diagnosis_category = field_for(Participant, 'diagnosis_category',
validate=enum_validation_generator(
DIAGNOSIS_CATEGORY_ENUM))
species = field_for(Participant, 'species',
validate=enum_validation_generator(
SPECIES_ENUM))
class Meta(BaseSchema.Meta):
model = Participant
resource_url = 'api.participants'
collection_url = 'api.participants_list'
exclude = (BaseSchema.Meta.exclude +
('study', 'family') +
('diagnoses', 'phenotypes', 'outcomes', 'biospecimens'))
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'study': ma.URLFor('api.studies', kf_id='<study_id>'),
'family': PatchedURLFor('api.families', kf_id='<family_id>'),
'diagnoses': ma.URLFor('api.diagnoses_list', participant_id='<kf_id>'),
'phenotypes': ma.URLFor('api.phenotypes_list',
participant_id='<kf_id>'),
'outcomes': ma.URLFor('api.outcomes_list',
participant_id='<kf_id>'),
'biospecimens': ma.URLFor('api.biospecimens_list',
participant_id='<kf_id>'),
'family_relationships': ma.URLFor('api.family_relationships_list',
participant_id='<kf_id>')
})
class CavaticaAppSchema(BaseSchema):
revision = field_for(CavaticaApp, 'revision',
validate=validate_positive_number)
github_commit_url = field_for(CavaticaApp, 'github_commit_url',
validate=URL())
class Meta(BaseSchema.Meta):
model = CavaticaApp
resource_url = 'api.cavatica_apps'
collection_url = 'api.cavatica_apps_list'
exclude = BaseSchema.Meta.exclude + ('tasks', )
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'tasks': ma.URLFor('api.tasks_list',
cavatica_app_id='<kf_id>')
})
class FamilySchema(BaseSchema):
family_type = field_for(
Family,
'family_type',
validate=enum_validation_generator(FAMILY_TYPE_ENUM))
class Meta(BaseSchema.Meta):
model = Family
resource_url = 'api.families'
collection_url = 'api.families_list'
exclude = BaseSchema.Meta.exclude + ('participants', )
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'participants':
ma.URLFor('api.participants_list', family_id='<kf_id>')
})
class PhenotypeSchema(BaseSchema):
participant_id = field_for(Phenotype, 'participant_id', required=True,
load_only=True, example='PT_DZB048J5')
age_at_event_days = field_for(Phenotype, 'age_at_event_days',
validate=validate_age, example=232)
observed = field_for(Phenotype, 'observed',
validate=enum_validation_generator(
OBSERVED_ENUM))
class Meta(BaseSchema.Meta):
model = Phenotype
resource_url = 'api.phenotypes'
collection_url = 'api.phenotypes_list'
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'participant': ma.URLFor('api.participants', kf_id='<participant_id>')
})
class ReadGroupGenomicFileSchema(BaseSchema):
read_group_id = field_for(ReadGroupGenomicFile, 'read_group_id',
required=True, load_only=True,
example='RF_ABB2C104')
genomic_file_id = field_for(ReadGroupGenomicFile, 'genomic_file_id',
required=True, load_only=True,
example='GF_ABB2C104')
class Meta(BaseSchema.Meta):
model = ReadGroupGenomicFile
resource_url = 'api.read_group_genomic_files'
collection_url = 'api.read_group_genomic_files_list'
exclude = BaseSchema.Meta.exclude + ('read_group', 'genomic_file')
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'read_group': ma.URLFor('api.read_groups',
kf_id='<read_group_id>'),
'genomic_file': ma.URLFor('api.genomic_files',
kf_id='<genomic_file_id>')
})
class SequencingCenterSchema(BaseSchema):
class Meta(BaseSchema.Meta):
resource_url = 'api.sequencing_centers'
collection_url = 'api.sequencing_centers_list'
model = SequencingCenter
exclude = BaseSchema.Meta.exclude + (
'biospecimens',
'sequencing_experiments',
)
_links = ma.Hyperlinks(
{
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'biospecimens':
ma.URLFor('api.biospecimens_list', sequencing_center_id='<kf_id>'),
'sequencing_experiments':
ma.URLFor('api.sequencing_experiments_list',
sequencing_center_id='<kf_id>')
},
description='Resource links and pagination')
class ReadGroupSchema(BaseSchema):
lane_number = field_for(ReadGroup, 'lane_number',
validate=validate_positive_number)
quality_scale = field_for(ReadGroup, 'quality_scale',
validate=enum_validation_generator(
QUALITY_SCALE_ENUM, common=True))
class Meta(BaseSchema.Meta):
resource_url = 'api.read_groups'
collection_url = 'api.read_groups_list'
model = ReadGroup
exclude = BaseSchema.Meta.exclude
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'read_group_genomic_files': ma.URLFor(
'api.read_group_genomic_files_list', read_group_id='<kf_id>'),
'genomic_files': ma.URLFor('api.genomic_files_list',
read_group_id='<kf_id>')
}, description='Resource links and pagination')
class StudySchema(BaseSchema):
investigator_id = field_for(Study, 'investigator_id',
required=False, load_only=True,
example='IG_ABB2C104')
release_status = field_for(Study, 'release_status',
validate=enum_validation_generator(
RELEASE_STATUS_ENUM))
class Meta(BaseSchema.Meta):
model = Study
resource_url = 'api.studies'
collection_url = 'api.studies_list'
exclude = BaseSchema.Meta.exclude + ('participants', 'study_files')
_links = ma.Hyperlinks({
'self': ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection': ma.URLFor(Meta.collection_url),
'investigator': PatchedURLFor('api.investigators',
kf_id='<investigator_id>'),
'participants': ma.URLFor('api.participants_list', study_id='<kf_id>'),
'study_files': ma.URLFor('api.study_files_list', study_id='<kf_id>')
})
class SequencingExperimentSchema(BaseSchema):
sequencing_center_id = field_for(SequencingExperiment,
'sequencing_center_id',
required=True,
load_only=True)
experiment_strategy = field_for(
SequencingExperiment,
'experiment_strategy',
validate=enum_validation_generator(EXPERIMENT_STRATEGY_ENUM))
platform = field_for(SequencingExperiment,
'platform',
validate=enum_validation_generator(PLATFORM_ENUM))
library_strand = field_for(
SequencingExperiment,
'library_strand',
validate=enum_validation_generator(LIBRARY_STRAND_ENUM))
library_selection = field_for(
SequencingExperiment,
'library_selection',
validate=enum_validation_generator(LIBRARY_SELECTION_ENUM))
library_prep = field_for(
SequencingExperiment,
'library_prep',
validate=enum_validation_generator(LIBRARY_PREP_ENUM))
class Meta(BaseSchema.Meta):
resource_url = 'api.sequencing_experiments'
collection_url = 'api.sequencing_experiments_list'
model = SequencingExperiment
exclude = (BaseSchema.Meta.exclude + ('sequencing_center', ) +
('genomic_files', ))
max_insert_size = field_for(SequencingExperiment,
'max_insert_size',
validate=validate_positive_number)
mean_insert_size = field_for(SequencingExperiment,
'mean_insert_size',
validate=validate_positive_number)
mean_depth = field_for(SequencingExperiment,
'mean_depth',
validate=validate_positive_number)
total_reads = field_for(SequencingExperiment,
'total_reads',
validate=validate_positive_number)
mean_read_length = field_for(SequencingExperiment,
'mean_read_length',
validate=validate_positive_number)
experiment_date = field_for(SequencingExperiment,
'experiment_date',
field_class=DateOrDatetime)
_links = ma.Hyperlinks(
{
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'sequencing_center':
ma.URLFor('api.sequencing_centers',
kf_id='<sequencing_center_id>'),
'sequencing_experiment_genomic_files':
ma.URLFor('api.sequencing_experiment_genomic_files_list',
sequencing_experiment_id='<kf_id>'),
'genomic_files':
ma.URLFor('api.genomic_files_list',
sequencing_experiment_id='<kf_id>')
},
description='Resource links and pagination')
class BiospecimenSchema(BaseSchema):
participant_id = field_for(Biospecimen,
'participant_id',
required=True,
load_only=True)
sequencing_center_id = field_for(Biospecimen,
'sequencing_center_id',
required=True,
load_only=True)
age_at_event_days = field_for(Biospecimen,
'age_at_event_days',
validate=validate_age)
concentration_mg_per_ml = field_for(Biospecimen,
'concentration_mg_per_ml',
validate=validate_positive_number)
volume_ul = field_for(Biospecimen,
'volume_ul',
validate=validate_positive_number)
shipment_date = field_for(Biospecimen,
'shipment_date',
field_class=DateOrDatetime)
analyte_type = field_for(
Biospecimen,
'analyte_type',
validate=enum_validation_generator(ANALYTE_TYPE_ENUM))
method_of_sample_procurement = field_for(
Biospecimen,
'method_of_sample_procurement',
validate=enum_validation_generator(SAMPLE_PROCUREMENT_ENUM))
duo_ids = field_for(Biospecimen,
'duo_ids',
validate=list_validation_generator(
DUO_ID_BIOSPECIMEN_ENUM, items_name='DUO IDs'))
class Meta(BaseSchema.Meta):
model = Biospecimen
resource_url = 'api.biospecimens'
collection_url = 'api.biospecimens_list'
exclude = (BaseSchema.Meta.exclude +
('participant', 'sequencing_center') +
('biospecimen_genomic_files', 'biospecimen_diagnoses'))
_links = ma.Hyperlinks({
'self':
ma.URLFor(Meta.resource_url, kf_id='<kf_id>'),
'collection':
ma.URLFor(Meta.collection_url),
'participant':
ma.URLFor('api.participants', kf_id='<participant_id>'),
'sequencing_center':
ma.URLFor('api.sequencing_centers', kf_id='<sequencing_center_id>'),
'biospecimen_genomic_files':
ma.URLFor('api.biospecimen_genomic_files_list',
biospecimen_id='<kf_id>'),
'biospecimen_diagnoses':
ma.URLFor('api.biospecimen_diagnoses_list', biospecimen_id='<kf_id>'),
'diagnoses':
ma.URLFor('api.diagnoses_list', biospecimen_id='<kf_id>'),
'genomic_files':
ma.URLFor('api.genomic_files_list', biospecimen_id='<kf_id>')
})
