class GeneticSpecimen(models.Model, IndexableMixin):
"""
Class to describe a biosample used for genomics testing or analysis.
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.GENETIC_SPECIMEN, "id"))
specimen_type = JSONField(validators=[ontology_validator],
help_text=rec_help(d.GENETIC_SPECIMEN,
"specimen_type"))
collection_body = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.GENETIC_SPECIMEN,
"collection_body"))
laterality = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.GENETIC_SPECIMEN,
"laterality"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.GENETIC_SPECIMEN,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class Variant(models.Model):
"""
Class to describe Individual variants or diagnosed causative variants
FHIR: Observation ?
Draft extension for Variant is in development
"""
ALLELE = (
('hgvsAllele', 'hgvsAllele'),
('vcfAllele', 'vcfAllele'),
('spdiAllele', 'spdiAllele'),
('iscnAllele', 'iscnAllele'),
)
allele_type = models.CharField(max_length=200, choices=ALLELE, help_text="One of four allele types.")
allele = JSONField(validators=[JsonSchemaValidator(schema=ALLELE_SCHEMA)],
help_text=rec_help(d.VARIANT, "allele"))
zygosity = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.VARIANT, "zygosity"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.VARIANT, "extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
class Disease(models.Model, IndexableMixin):
"""
Class to represent a diagnosis and inference or hypothesis about the cause
underlying the observed phenotypic abnormalities
FHIR: Condition
"""
term = JSONField(validators=[ontology_validator], help_text=rec_help(d.DISEASE, "term"))
# "ageOfOnset": {
# "age": "P38Y7M"
# }
# OR
# "ageOfOnset": {
# "id": "HP:0003581",
# "label": "Adult onset"
# }
onset = JSONField(blank=True, null=True, validators=[JsonSchemaValidator(schema=PHENOPACKET_DISEASE_ONSET_SCHEMA)],
help_text=rec_help(d.DISEASE, "onset"))
disease_stage = JSONField(blank=True, null=True, validators=[ontology_list_validator],
help_text=rec_help(d.DISEASE, "disease_stage"))
tnm_finding = JSONField(blank=True, null=True, validators=[ontology_list_validator],
help_text=rec_help(d.DISEASE, "tnm_finding"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.DISEASE, "extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
class LabsVital(models.Model, IndexableMixin):
"""
Class to record tests performed on patient.
"""
# TODO Should this class be a part of Patients app? patient related metadata
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.LABS_VITAL, "id"))
individual = models.ForeignKey(Individual,
on_delete=models.CASCADE,
help_text=rec_help(d.LABS_VITAL,
"individual"))
# TODO Change CodeableConcept to Ontology class
tumor_marker_code = JSONField(validators=[ontology_validator],
help_text=rec_help(d.LABS_VITAL,
"tumor_marker_code"))
tumor_marker_data_value = JSONField(
blank=True,
null=True,
validators=[tumor_marker_data_value_validator],
help_text=rec_help(d.LABS_VITAL, "tumor_marker_data_value"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.LABS_VITAL,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class ExperimentResult(models.Model, IndexableMixin):
""" Class to represent information about analysis of sequencing data in a file format. """
# TODO identifier assigned by lab (?)
identifier = CharField(max_length=200, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "identifier"))
description = CharField(max_length=500, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "description"))
filename = CharField(max_length=500, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "filename"))
genome_assembly_id = CharField(max_length=50, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "genome_assembly_id"))
file_format = CharField(max_length=50, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "file_format"))
data_output_type = CharField(max_length=200, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "data_output_type"))
usage = CharField(max_length=200, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "usage"))
creation_date = CharField(max_length=500, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "creation_date"))
created_by = CharField(max_length=200, blank=True, null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "created_by"))
extra_properties = JSONField(blank=True, default=dict, validators=[key_value_validator],
help_text=rec_help(d.EXPERIMENT_RESULT, "extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.identifier)
class Instrument(models.Model, IndexableMixin):
""" Class to represent information about instrument used to perform a sequencing experiment. """
# TODO identifier assigned by lab (?)
identifier = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"identifier"))
platform = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.INSTRUMENT, "platform"))
description = CharField(max_length=500,
blank=True,
null=True,
help_text=rec_help(d.INSTRUMENT, "description"))
model = CharField(max_length=500,
blank=True,
null=True,
help_text=rec_help(d.INSTRUMENT, "model"))
extra_properties = JSONField(blank=True,
default=dict,
validators=[key_value_validator],
help_text=rec_help(d.INSTRUMENT,
"extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
class CancerCondition(models.Model, IndexableMixin):
"""
Class to record the history of primary or secondary cancer conditions.
"""
CANCER_CONDITION_TYPE = (('primary', 'primary'), ('secondary',
'secondary'))
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.CANCER_CONDITION, "id"))
condition_type = models.CharField(choices=CANCER_CONDITION_TYPE,
max_length=200,
help_text=rec_help(
d.CANCER_CONDITION,
"condition_type"))
body_site = JSONField(null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.CANCER_CONDITION, 'body_site'))
laterality = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_CONDITION,
"laterality"))
clinical_status = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_CONDITION,
"clinical_status"))
code = JSONField(validators=[ontology_validator],
help_text=rec_help(d.CANCER_CONDITION, "code"))
date_of_diagnosis = models.DateTimeField(blank=True,
null=True,
help_text=rec_help(
d.CANCER_CONDITION,
"date_of_diagnosis"))
histology_morphology_behavior = JSONField(
blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_CONDITION,
"histology_morphology_behavior"))
verification_status = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_CONDITION,
"verification_status"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.CANCER_CONDITION,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class Phenopacket(models.Model, IndexableMixin):
"""
Class to aggregate Individual's experiments data
FHIR: Composition
"""
id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.PHENOPACKET, "id"))
# if Individual instance is deleted Phenopacket instance is deleted too
# CHECK !!! Force as required?
subject = models.ForeignKey(
Individual, on_delete=models.CASCADE, related_name="phenopackets",
help_text=rec_help(d.PHENOPACKET, "subject"))
# PhenotypicFeatures are present in Biosample, so can be accessed via Biosample instance
# phenotypic_features = models.ManyToManyField(PhenotypicFeature, blank=True,
# help_text='Phenotypic features observed in the proband.')
biosamples = models.ManyToManyField(Biosample, blank=True, help_text=rec_help(d.PHENOPACKET, "biosamples"))
genes = models.ManyToManyField(Gene, blank=True, help_text=rec_help(d.PHENOPACKET, "genes"))
variants = models.ManyToManyField(Variant, blank=True, help_text=rec_help(d.PHENOPACKET, "variants"))
diseases = models.ManyToManyField(Disease, blank=True, help_text=rec_help(d.PHENOPACKET, "diseases"))
hts_files = models.ManyToManyField(HtsFile, blank=True, help_text=rec_help(d.PHENOPACKET, "hts_files"))
# TODO OneToOneField
meta_data = models.ForeignKey(MetaData, on_delete=models.CASCADE, help_text=rec_help(d.PHENOPACKET, "meta_data"))
table = models.ForeignKey("chord.Table", on_delete=models.CASCADE, blank=True, null=True) # TODO: Help text
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.PHENOPACKET, "extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
class MCodePacket(models.Model, IndexableMixin):
"""
Class to aggregate Individual's cancer related metadata
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.MCODEPACKET, "id"))
subject = models.ForeignKey(Individual,
on_delete=models.CASCADE,
help_text=rec_help(d.MCODEPACKET, "subject"))
genomics_report = models.ForeignKey(GenomicsReport,
blank=True,
null=True,
on_delete=models.SET_NULL,
help_text=rec_help(
d.MCODEPACKET, "genomics_report"))
cancer_condition = models.ManyToManyField(CancerCondition,
blank=True,
help_text=rec_help(
d.MCODEPACKET,
"cancer_condition"))
cancer_related_procedures = models.ManyToManyField(
CancerRelatedProcedure,
blank=True,
help_text=rec_help(d.MCODEPACKET, "cancer_related_procedures"))
medication_statement = models.ManyToManyField(MedicationStatement,
blank=True,
help_text=rec_help(
d.MCODEPACKET,
"medication_statement"))
date_of_death = models.CharField(max_length=200,
blank=True,
help_text=rec_help(
d.MCODEPACKET, "date_of_death"))
cancer_disease_status = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(
d.MCODEPACKET,
"cancer_disease_status"))
# link to dataset via the table
table = models.ForeignKey("chord.Table",
on_delete=models.CASCADE,
blank=True,
null=True) # TODO: Help text
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.MCODEPACKET,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class PhenotypicFeature(models.Model, IndexableMixin):
"""
Class to describe a phenotype of an Individual
FHIR: Condition or Observation
"""
description = models.CharField(max_length=200, blank=True, help_text=rec_help(d.PHENOTYPIC_FEATURE, "description"))
pftype = JSONField(verbose_name='type', validators=[ontology_validator],
help_text=rec_help(d.PHENOTYPIC_FEATURE, "type"))
negated = models.BooleanField(default=False, help_text=rec_help(d.PHENOTYPIC_FEATURE, "negated"))
severity = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.PHENOTYPIC_FEATURE, "severity"))
modifier = JSONField(blank=True, null=True, validators=[ontology_list_validator],
help_text=rec_help(d.PHENOTYPIC_FEATURE, "modifier"))
onset = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.PHENOTYPIC_FEATURE, "onset"))
# evidence can stay here because evidence is given for an observation of PF
# JSON schema to check evidence_code is present
# FHIR: Condition.evidence
evidence = JSONField(blank=True, null=True, validators=[JsonSchemaValidator(schema=PHENOPACKET_EVIDENCE_SCHEMA)],
help_text=rec_help(d.PHENOTYPIC_FEATURE, "evidence"))
biosample = models.ForeignKey(
"Biosample", on_delete=models.SET_NULL, blank=True, null=True, related_name='phenotypic_features')
phenopacket = models.ForeignKey(
"Phenopacket", on_delete=models.SET_NULL, blank=True, null=True, related_name='phenotypic_features')
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.PHENOTYPIC_FEATURE, "extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class CancerRelatedProcedure(models.Model, IndexableMixin):
"""
Class to represent radiological treatment or surgical action addressing a cancer condition.
"""
PROCEDURE_TYPES = (('radiation', 'radiation'), ('surgical', 'surgical'))
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "id"))
procedure_type = models.CharField(choices=PROCEDURE_TYPES,
max_length=200,
help_text=rec_help(
d.CANCER_RELATED_PROCEDURE,
"procedure_type"))
code = JSONField(validators=[ontology_validator],
help_text=rec_help(d.CANCER_RELATED_PROCEDURE, "code"))
body_site = JSONField(null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.CANCER_RELATED_PROCEDURE,
'body_site'))
laterality = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_RELATED_PROCEDURE,
"laterality"))
treatment_intent = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_RELATED_PROCEDURE,
"treatment_intent"))
# Only for Surgical Procedure
# TODO CHANGE to ontology list validator
reason_code = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_RELATED_PROCEDURE,
"reason_code"))
reason_reference = models.ManyToManyField(CancerCondition,
blank=True,
help_text=rec_help(
d.CANCER_RELATED_PROCEDURE,
"reason_reference"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.CANCER_RELATED_PROCEDURE,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class Procedure(models.Model):
"""
Class to represent a clinical procedure performed on an individual
(subject) in order to extract a biosample
FHIR: Procedure
"""
code = JSONField(help_text=rec_help(d.PROCEDURE, "code"))
body_site = JSONField(blank=True, null=True, help_text=rec_help(d.PROCEDURE, "body_site"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.PROCEDURE, "extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class MetaData(models.Model):
"""
Class to store structured definitions of the resources
and ontologies used within the phenopacket
FHIR: Metadata
"""
created = models.DateTimeField(default=timezone.now, help_text=rec_help(d.META_DATA, "created"))
created_by = models.CharField(max_length=200, help_text=rec_help(d.META_DATA, "created_by"))
submitted_by = models.CharField(max_length=200, blank=True, help_text=rec_help(d.META_DATA, "submitted_by"))
resources = models.ManyToManyField(Resource, help_text=rec_help(d.META_DATA, "resources"))
updates = ArrayField(
JSONField(null=True, blank=True), blank=True, null=True,
help_text=rec_help(d.META_DATA, "updates"))
phenopacket_schema_version = models.CharField(max_length=200, blank=True,
help_text='Schema version of the current phenopacket.')
external_references = ArrayField(
JSONField(null=True, blank=True), blank=True, null=True,
help_text=rec_help(d.META_DATA, "external_references"))
extra_properties = JSONField(
blank=True, null=True, help_text=rec_help(d.META_DATA, "extra_properties"))
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class MetaData(models.Model):
"""
Class to store structured definitions of the resources
and ontologies used within the phenopacket
FHIR: Metadata
"""
created = models.DateTimeField(default=timezone.now, help_text=rec_help(d.META_DATA, "created"))
created_by = models.CharField(max_length=200, help_text=rec_help(d.META_DATA, "created_by"))
submitted_by = models.CharField(max_length=200, blank=True, help_text=rec_help(d.META_DATA, "submitted_by"))
resources = models.ManyToManyField(Resource, help_text=rec_help(d.META_DATA, "resources"))
updates = JSONField(blank=True, null=True, validators=[JsonSchemaValidator(
schema=schema_list(PHENOPACKET_UPDATE_SCHEMA), formats=['date-time'])],
help_text=rec_help(d.META_DATA, "updates"))
phenopacket_schema_version = models.CharField(max_length=200, blank=True,
help_text='Schema version of the current phenopacket.')
external_references = JSONField(blank=True, null=True, validators=[JsonSchemaValidator(
schema=schema_list(PHENOPACKET_EXTERNAL_REFERENCE_SCHEMA))],
help_text=rec_help(d.META_DATA, "external_references"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.META_DATA, "extra_properties"))
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class GenomicRegionStudied(models.Model, IndexableMixin):
"""
Class to describe the area of the genome region referenced in testing for variants.
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.GENOMIC_REGION_STUDIED, "id"))
# TODO schema Range list
dna_ranges_examined = JSONField(blank=True,
null=True,
validators=[ontology_list_validator],
help_text=rec_help(
d.GENOMIC_REGION_STUDIED,
"dna_ranges_examined"))
dna_region_description = ArrayField(models.CharField(
max_length=100,
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
'dna_region_description')),
blank=True,
default=list)
gene_mutation = JSONField(blank=True,
null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
"gene_mutation"))
# TODO check: thisis not a Reference in mcode data dictionary why not?
gene_studied = JSONField(blank=True,
null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
"gene_studied"))
genomic_reference_sequence_id = JSONField(
blank=True,
null=True,
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
"genomic_reference_sequence_id"))
genomic_region_coordinate_system = JSONField(
blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
"genomic_region_coordinate_system"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.GENOMIC_REGION_STUDIED,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class Gene(models.Model):
"""
Class to represent an identifier for a gene
FHIR: ?
Draft extension for Gene is in development
where Gene defined via class CodeableConcept
"""
# Gene id is unique
id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.GENE, "id"))
# CURIE style? Yes!
alternate_ids = ArrayField(models.CharField(max_length=200, blank=True), blank=True, default=list,
help_text=rec_help(d.GENE, "alternate_ids"))
symbol = models.CharField(max_length=200, help_text=rec_help(d.GENE, "symbol"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.GENE, "extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class HtsFile(models.Model, IndexableMixin):
"""
Class to link HTC files with data
FHIR: DocumentReference
"""
HTS_FORMAT = (
('UNKNOWN', 'UNKNOWN'),
('SAM', 'SAM'),
('BAM', 'BAM'),
('CRAM', 'CRAM'),
('VCF', 'VCF'),
('BCF', 'BCF'),
('GVCF', 'GVCF'),
)
uri = models.URLField(primary_key=True, max_length=200, help_text=rec_help(d.HTS_FILE, "uri"))
description = models.CharField(max_length=200, blank=True, help_text=rec_help(d.HTS_FILE, "description"))
hts_format = models.CharField(max_length=200, choices=HTS_FORMAT, help_text=rec_help(d.HTS_FILE, "hts_format"))
genome_assembly = models.CharField(max_length=200, help_text=rec_help(d.HTS_FILE, "genome_assembly"))
# e.g.
# "individualToSampleIdentifiers": {
# "patient23456": "NA12345"
# TODO how to perform this validation, ensure the patient id is the correct one?
individual_to_sample_identifiers = JSONField(
blank=True, null=True, help_text=rec_help(d.HTS_FILE, "individual_to_sample_identifiers"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.HTS_FILE, "extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.uri)
class Resource(models.Model):
"""
Class to represent a description of an external resource
used for referencing an object
FHIR: CodeSystem
"""
class Meta:
unique_together = (("namespace_prefix", "version"), )
# resource_id e.g. "id": "uniprot:2019_07"
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.RESOURCE, "id"))
name = models.CharField(max_length=200,
help_text=rec_help(d.RESOURCE, "name"))
namespace_prefix = models.CharField(max_length=200,
help_text=rec_help(
d.RESOURCE, "namespace_prefix"))
url = models.URLField(max_length=200,
help_text=rec_help(d.RESOURCE, "url"))
version = models.CharField(max_length=200,
help_text=rec_help(d.RESOURCE, "version"))
iri_prefix = models.URLField(max_length=200,
help_text=rec_help(d.RESOURCE, "iri_prefix"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.RESOURCE,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def clean(self):
# For phenopackets compliance, we need to have a string identifier. Django does not allow compound keys, we
# ideally want to identify resources by the pair (namespace_prefix, version). In this case, we hack this by
# enforcing that id == (namespace_prefix, version). In the case of an unspecified version, enforce
# id == namespace_prefix.
if (self.version and self.id != f"{self.namespace_prefix}:{self.version}") or \
(not self.version and self.id != self.namespace_prefix):
raise ValidationError({
"id": [
ValidationError(
"Resource ID must match the format 'namespace_prefix:version'"
)
],
})
def save(self, *args, **kwargs):
self.clean()
return super().save(*args, **kwargs)
def __str__(self):
return str(self.id)
class GenomicsReport(models.Model, IndexableMixin):
"""
Genetic Analysis Summary.
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.GENOMICS_REPORT, "id"))
code = JSONField(validators=[ontology_validator],
help_text=rec_help(d.GENOMICS_REPORT, "code"))
performing_organization_name = models.CharField(
max_length=200,
blank=True,
help_text=rec_help(d.GENOMICS_REPORT, "performing_organization_name"))
issued = models.DateTimeField(default=timezone.now,
help_text=rec_help(d.GENOMICS_REPORT,
"issued"))
genetic_specimen = models.ManyToManyField(GeneticSpecimen,
blank=True,
help_text=rec_help(
d.GENOMICS_REPORT,
"genetic_specimen"))
genetic_variant = models.ForeignKey(CancerGeneticVariant,
blank=True,
null=True,
on_delete=models.SET_NULL,
help_text=rec_help(
d.GENOMICS_REPORT,
"genetic_variant"))
genomic_region_studied = models.ForeignKey(GenomicRegionStudied,
blank=True,
null=True,
on_delete=models.SET_NULL,
help_text=rec_help(
d.GENOMICS_REPORT,
"genomic_region_studied"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.GENOMICS_REPORT,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class TNMStaging(models.Model, IndexableMixin):
"""
Class to describe the spread of cancer in a patient’s body.
"""
TNM_TYPES = (('clinical', 'clinical'), ('pathologic', 'pathologic'))
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.TNM_STAGING, "id"))
tnm_type = models.CharField(choices=TNM_TYPES,
max_length=200,
help_text=rec_help(d.TNM_STAGING, "tnm_type"))
stage_group = JSONField(validators=[complex_ontology_validator],
help_text=rec_help(d.TNM_STAGING, "stage_group"))
primary_tumor_category = JSONField(validators=[complex_ontology_validator],
help_text=rec_help(
d.TNM_STAGING,
"primary_tumor_category"))
regional_nodes_category = JSONField(
validators=[complex_ontology_validator],
help_text=rec_help(d.TNM_STAGING, "regional_nodes_category"))
distant_metastases_category = JSONField(
validators=[complex_ontology_validator],
help_text=rec_help(d.TNM_STAGING, "distant_metastases_category"))
# TODO check if one cancer condition has many TNM Staging
cancer_condition = models.ForeignKey(CancerCondition,
on_delete=models.CASCADE,
help_text=rec_help(
d.TNM_STAGING,
"cancer_condition"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.TNM_STAGING,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class MedicationStatement(models.Model, IndexableMixin):
"""
Class to record the use of a medication.
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.MEDICATION_STATEMENT, "id"))
# list http://hl7.org/fhir/us/core/STU3.1/ValueSet-us-core-medication-codes.html
medication_code = JSONField(validators=[ontology_validator],
help_text=rec_help(d.MEDICATION_STATEMENT,
"medication_code"))
termination_reason = JSONField(null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.MEDICATION_STATEMENT,
'termination_reason'))
treatment_intent = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.MEDICATION_STATEMENT,
"treatment_intent"))
start_date = models.DateTimeField(blank=True,
null=True,
help_text=rec_help(
d.MEDICATION_STATEMENT,
"start_date"))
end_date = models.DateTimeField(blank=True,
null=True,
help_text=rec_help(d.MEDICATION_STATEMENT,
"end_date"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.MEDICATION_STATEMENT,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
class Resource(models.Model):
"""
Class to represent a description of an external resource
used for referencing an object
FHIR: CodeSystem
"""
# resource_id e.g. "id": "uniprot"
id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.RESOURCE, "id"))
name = models.CharField(max_length=200, help_text=rec_help(d.RESOURCE, "name"))
namespace_prefix = models.CharField(max_length=200, help_text=rec_help(d.RESOURCE, "namespace_prefix"))
url = models.URLField(max_length=200, help_text=rec_help(d.RESOURCE, "url"))
version = models.CharField(max_length=200, help_text=rec_help(d.RESOURCE, "version"))
iri_prefix = models.URLField(max_length=200, help_text=rec_help(d.RESOURCE, "iri_prefix"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.RESOURCE, "extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
def __str__(self):
return str(self.id)
class Experiment(models.Model, IndexableMixin):
""" Class to store Experiment information """
LIBRARY_STRATEGY = (
('DNase-Hypersensitivity', 'DNase-Hypersensitivity'),
('ATAC-seq', 'ATAC-seq'),
('NOME-Seq', 'NOME-Seq'),
('Bisulfite-Seq', 'Bisulfite-Seq'),
('MeDIP-Seq', 'MeDIP-Seq'),
('MRE-Seq', 'MRE-Seq'),
('ChIP-Seq', 'ChIP-Seq'),
('RNA-Seq', 'RNA-Seq'),
('miRNA-Seq', 'miRNA-Seq'),
('WGS', 'WGS'),
)
MOLECULE = (
('total RNA', 'total RNA'),
('polyA RNA', 'polyA RNA'),
('cytoplasmic RNA', 'cytoplasmic RNA'),
('nuclear RNA', 'nuclear RNA'),
('small RNA', 'small RNA'),
('genomic DNA', 'genomic DNA'),
('protein', 'protein'),
('other', 'other'),
)
id = CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.EXPERIMENT, 'id'))
reference_registry_id = CharField(max_length=30,
blank=True,
null=True,
help_text=rec_help(
d.EXPERIMENT,
'reference_registry_id'))
qc_flags = ArrayField(CharField(max_length=100,
help_text=rec_help(d.EXPERIMENT,
'qc_flags')),
blank=True,
default=list)
experiment_type = CharField(max_length=30,
help_text=rec_help(d.EXPERIMENT,
'experiment_type'))
experiment_ontology = JSONField(blank=True,
default=list,
validators=[ontology_list_validator],
help_text=rec_help(d.EXPERIMENT,
'experiment_ontology'))
molecule_ontology = JSONField(blank=True,
default=list,
validators=[ontology_list_validator],
help_text=rec_help(d.EXPERIMENT,
'molecule_ontology'))
molecule = CharField(choices=MOLECULE,
max_length=20,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT, 'molecule'))
library_strategy = CharField(choices=LIBRARY_STRATEGY,
max_length=25,
help_text=rec_help(d.EXPERIMENT,
'library_strategy'))
other_fields = JSONField(blank=True,
default=dict,
validators=[key_value_validator],
help_text=rec_help(d.EXPERIMENT, 'other_fields'))
biosample = models.ForeignKey(Biosample,
on_delete=models.CASCADE,
help_text=rec_help(d.EXPERIMENT,
'biosample'))
table = models.ForeignKey("chord.Table",
on_delete=models.CASCADE,
blank=True,
null=True) # TODO: Help text
def __str__(self):
return str(self.id)
class Experiment(models.Model, IndexableMixin):
""" Class to store Experiment information """
id = CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.EXPERIMENT, "id"))
# STUDY TYPE
# ["Whole Genome Sequencing","Metagenomics","Transcriptome Analysis","Resequencing","Epigenetics",
# "Synthetic Genomics","Forensic or Paleo-genomics","Gene Regulation Study","Cancer Genomics",
# "Population Genomics","RNASeq","Pooled Clone Sequencing","Transcriptome Sequencing","Other"]
study_type = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT, "study_type"))
# TYPE
experiment_type = CharField(max_length=200,
help_text=rec_help(d.EXPERIMENT,
"experiment_type"))
experiment_ontology = JSONField(blank=True,
default=list,
validators=[ontology_list_validator],
help_text=rec_help(d.EXPERIMENT,
"experiment_ontology"))
# MOLECULE
molecule = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT, "molecule"))
molecule_ontology = JSONField(blank=True,
default=list,
validators=[ontology_list_validator],
help_text=rec_help(d.EXPERIMENT,
"molecule_ontology"))
# LIBRARY
library_strategy = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT,
"library_strategy"))
library_source = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT,
"library_source"))
library_selection = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT,
"library_selection"))
library_layout = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT,
"library_layout"))
extraction_protocol = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT,
"extraction_protocol"))
reference_registry_id = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(
d.EXPERIMENT,
"reference_registry_id"))
qc_flags = ArrayField(CharField(max_length=200,
help_text=rec_help(d.EXPERIMENT,
"qc_flags")),
blank=True,
default=list)
# SAMPLE
biosample = models.ForeignKey(Biosample,
on_delete=models.CASCADE,
help_text=rec_help(d.EXPERIMENT,
"biosample"))
table = models.ForeignKey("chord.Table",
on_delete=models.CASCADE,
blank=True,
null=True) # TODO: Help text
# EXPERIMENT RESULT
experiment_results = models.ManyToManyField("ExperimentResult",
blank=True,
help_text=rec_help(
d.EXPERIMENT,
"experiment_results"))
# INTSRUMENT
instrument = models.ForeignKey("Instrument",
blank=True,
null=True,
on_delete=models.CASCADE,
help_text=rec_help(d.EXPERIMENT,
"instrument"))
# EXTRA
extra_properties = JSONField(blank=True,
default=dict,
validators=[key_value_validator],
help_text=rec_help(d.EXPERIMENT,
"extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
class ExperimentResult(models.Model, IndexableMixin):
""" Class to represent information about analysis of sequencing data in a file format. """
FILE_FORMAT = (
("SAM", "SAM"),
("BAM", "BAM"),
("CRAM", "CRAM"),
("BAI", "BAI"),
("CRAI", "CRAI"),
("VCF", "VCF"),
("BCF", "BCF"),
("GVCF", "GVCF"),
("BigWig", "BigWig"),
("BigBed", "BigBed"),
("FASTA", "FASTA"),
("FASTQ", "FASTQ"),
("TAB", "TAB"),
("SRA", "SRA"),
("SRF", "SRF"),
("SFF", "SFF"),
("GFF", "GFF"),
("TABIX", "TABIX"),
("UNKNOWN", "UNKNOWN"),
("OTHER", "OTHER"),
)
# TODO or Processed/Sequenced vs. Raw/Derived
DATA_OUTPUT_TYPE = (
("Raw data", "Raw data"),
("Derived data", "Derived data"),
)
# Data usage
# USAGE = (
# ("Visualize", "Visualize"),
# ("Download", "Download"),
# )
# TODO identifier assigned by lab (?)
identifier = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"identifier"))
description = CharField(max_length=500,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"description"))
filename = CharField(max_length=500,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "filename"))
file_format = CharField(max_length=50,
choices=FILE_FORMAT,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"file_format"))
data_output_type = CharField(max_length=50,
choices=DATA_OUTPUT_TYPE,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"data_output_type"))
usage = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT, "usage"))
creation_date = CharField(max_length=500,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"creation_date"))
created_by = CharField(max_length=200,
blank=True,
null=True,
help_text=rec_help(d.EXPERIMENT_RESULT,
"created_by"))
extra_properties = JSONField(blank=True,
default=dict,
validators=[key_value_validator],
help_text=rec_help(d.EXPERIMENT_RESULT,
"extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.identifier)
class Biosample(models.Model, IndexableMixin):
"""
Class to describe a unit of biological material
FHIR: Specimen
"""
id = models.CharField(primary_key=True, max_length=200, help_text=rec_help(d.BIOSAMPLE, "id"))
# if Individual instance is deleted Biosample instance is deleted too
individual = models.ForeignKey(
Individual, on_delete=models.CASCADE, blank=True, null=True, related_name="biosamples",
help_text=rec_help(d.BIOSAMPLE, "individual_id"))
description = models.CharField(max_length=200, blank=True, help_text=rec_help(d.BIOSAMPLE, "description"))
sampled_tissue = JSONField(validators=[ontology_validator], help_text=rec_help(d.BIOSAMPLE, "sampled_tissue"))
# phenotypic_features = models.ManyToManyField(PhenotypicFeature, blank=True,
# help_text='List of phenotypic abnormalities of the sample.')
taxonomy = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.BIOSAMPLE, "taxonomy"))
# An ISO8601 string represent age
individual_age_at_collection = JSONField(blank=True, null=True, validators=[age_or_age_range_validator],
help_text=rec_help("individual_age_at_collection"))
histological_diagnosis = JSONField(
blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.BIOSAMPLE, "histological_diagnosis"))
# TODO: Lists?
tumor_progression = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.BIOSAMPLE, "tumor_progression"))
tumor_grade = JSONField(blank=True, null=True, validators=[ontology_validator],
help_text=rec_help(d.BIOSAMPLE, "tumor_grade"))
diagnostic_markers = JSONField(blank=True, null=True, validators=[ontology_list_validator],
help_text=rec_help(d.BIOSAMPLE, "diagnostic_markers"))
# CHECK! if Procedure instance is deleted Biosample instance is deleted too
procedure = models.ForeignKey(Procedure, on_delete=models.CASCADE, help_text=rec_help(d.BIOSAMPLE, "procedure"))
hts_files = models.ManyToManyField(
HtsFile, blank=True, related_name='biosample_hts_files', help_text=rec_help(d.BIOSAMPLE, "hts_files"))
variants = models.ManyToManyField(Variant, blank=True, help_text=rec_help(d.BIOSAMPLE, "variants"))
is_control_sample = models.BooleanField(default=False, help_text=rec_help(d.BIOSAMPLE, "is_control_sample"))
extra_properties = JSONField(blank=True, null=True, help_text=rec_help(d.BIOSAMPLE, "extra_properties"))
created = models.DateTimeField(auto_now_add=True)
updated = models.DateTimeField(auto_now=True)
def __str__(self):
return str(self.id)
@property
def get_sample_tissue_data(self):
return {'reference': {
'reference': self.sampled_tissue.get('id'),
'display': self.sampled_tissue.get('label')
}
}
class CancerGeneticVariant(models.Model, IndexableMixin):
"""
Class to record an alteration in DNA.
"""
id = models.CharField(primary_key=True,
max_length=200,
help_text=rec_help(d.CANCER_GENETIC_VARIANT, "id"))
data_value = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_GENETIC_VARIANT,
"data_value"))
method = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_GENETIC_VARIANT, "method"))
amino_acid_change = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_GENETIC_VARIANT,
"amino_acid_change"))
amino_acid_change_type = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(
d.CANCER_GENETIC_VARIANT,
"amino_acid_change_type"))
cytogenetic_location = JSONField(blank=True,
null=True,
help_text=rec_help(
d.CANCER_GENETIC_VARIANT,
"cytogenetic_location"))
cytogenetic_nomenclature = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(
d.CANCER_GENETIC_VARIANT,
"cytogenetic_nomenclature"))
gene_studied = models.ManyToManyField(Gene,
blank=True,
help_text=rec_help(
d.CANCER_GENETIC_VARIANT,
"gene_studied"))
genomic_dna_change = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(d.CANCER_GENETIC_VARIANT,
"genomic_dna_change"))
genomic_source_class = JSONField(blank=True,
null=True,
validators=[ontology_validator],
help_text=rec_help(
d.CANCER_GENETIC_VARIANT,
"genomic_source_class"))
variation_code = JSONField(blank=True,
null=True,
validators=[ontology_list_validator],
help_text=rec_help(d.CANCER_GENETIC_VARIANT,
"variation_code"))
extra_properties = JSONField(blank=True,
null=True,
help_text=rec_help(d.CANCER_GENETIC_VARIANT,
"extra_properties"))
created = models.DateTimeField(auto_now=True)
updated = models.DateTimeField(auto_now_add=True)
class Meta:
ordering = ['id']
def __str__(self):
return str(self.id)
