Converters¶
-
converters.resources.
age_to_fhir
(obj, mapping, field)¶ Generic function to convert Phenopackets Age or AgeRange to FHIR Age.
- Parameters
obj – object to which field Age or AgeRange belongs to
mapping – mapping from PHENOPACKETS_ON_FHIR
field – name of the field that stores age
- Returns
age extension object
-
converters.resources.
biosample_to_fhir
(obj)¶ Converts Biosample to FHIR Specimen.
- Parameters
obj – Biosample json
- Returns
FHIR Specimen json
-
converters.resources.
check_disease_onset
(disease)¶ Phenopackets schema allows age to be represented by ISO8601 string, whereis Pheno-FHIR guide requires it to be represented by CodeableConcept. This function checks how age is represented in data.
- Parameters
disease – disease json object
- Returns
True/False
-
converters.resources.
codeable_concepts_fields
(field_list, profile, obj)¶ Converts a list of fields to FHIR CodeableConcepts and returns a list of extensions.
- Parameters
field_list – fields to convert to codeable concepts
profile – name of an object in phenopackets mappings
obj – object to which fields belong to
- Returns
list of extensions
-
converters.resources.
disease_to_fhir
(obj)¶ Converts Disease to FHIR Condition.
- Parameters
obj – Disease json
- Returns
FHIR Condition json
-
converters.resources.
fhir_codeable_concept
(obj)¶ Generic function to convert object to FHIR CodeableConcept.
-
converters.resources.
fhir_coding_util
(obj)¶ Genenric function to convert object to FHIR Coding.
-
converters.resources.
gene_to_fhir
(obj)¶ Convert Gene to Observation.component:gene property. GA4GH Phenopackets Implementation Guide provides a link to Genomics Reporting Implementation Guide (STU1) mapping http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied .
- Parameters
obj – gene json
- Returns
Observation.component:gene json
-
converters.resources.
hts_file_to_fhir
(obj)¶ Converts HTS file to FHIR DocumentReference.
- Parameters
obj – HTS file json
- Returns
FHIR DocumentReference json
-
converters.resources.
individual_to_fhir
(obj)¶ Converts Individual to FHIR Patient.
- Parameters
obj – Individual json
- Returns
FHIR Patient json
-
converters.resources.
phenopacket_to_fhir
(obj)¶ Converts Phenopacket to FHIR Composition.
- Parameters
obj – Phenopacket json
- Returns
FHIR Composition json
-
converters.resources.
phenotypic_feature_to_fhir
(obj)¶ Converts Phenotypic feature to FHIR Observation.
- Parameters
obj – PhenotypicFeature json
- Returns
FHIR Observation json
-
converters.resources.
procedure_to_fhir
(obj)¶ Converts Procedure to FHIR Specimen collection.
-
converters.resources.
variant_to_fhir
(obj)¶ Variant corresponds to Observation.component:variant. GA4GH Phenopackets Implementation Guide provides a link to Genomics Reporting Implementation Guide (STU1) mapping http://hl7.org/fhir/uv/genomics-reporting/STU1/variant.html.
- Parameters
obj – Variant json
- Returns
Observation.component:variant json