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834 message parser meta data #853

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merged 9 commits into from
Oct 10, 2023
Merged

834 message parser meta data #853

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1cfb4e4
wip
nickbristow Oct 4, 2023
86cb0f9
adds an option to parse_message to include meta data
nickbristow Oct 5, 2023
972d902
Merge branch 'main' into 834-message-parser-meta-data
nickbristow Oct 5, 2023
82def4f
Update main.py
nickbristow Oct 5, 2023
5afc858
Update test_parse_message_endpoint.py
nickbristow Oct 5, 2023
de8e436
add optional metadata
nickbristow Oct 6, 2023
c335d17
Merge branch 'main' into 834-message-parser-meta-data
nickbristow Oct 6, 2023
82e2ff8
Update utils.py
nickbristow Oct 6, 2023
38c18ef
Update main.py
nickbristow Oct 6, 2023
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366 changes: 366 additions & 0 deletions containers/message-parser/app/default_schemas/ecr_with_metadata.json
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{
"patient_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Patient').id",
"data_type": "string",
"nullable": false
},
"person_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Person').id",
"data_type": "string",
"nullable": false
},
"last_name": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').name.first().family",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"first_name": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').name.first().given.first()",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"birth_date": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').birthDate",
"data_type": "date",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"gender": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').gender",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"race": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race').extension.valueCoding.display",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"ethnicity": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity').extension.valueCoding.display",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"street_address1": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.line[0]",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"street_address2": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.line[1]",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"state": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.state",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"zip": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.postalCode",
"data_type": "string",
"nullable": true,
"metadata": {
"category": "Personal info"
}
},
"latitude": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.extension.where(url='http://hl7.org/fhir/StructureDefinition/geolocation').extension.where(url='latitude').valueDecimal",
"data_type": "float",
"nullable": true
},
"longitude": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').address.extension.where(url='http://hl7.org/fhir/StructureDefinition/geolocation').extension.where(url='longitude').valueDecimal",
"data_type": "float",
"nullable": true
},
"rr_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Composition').section.where(title = 'Reportability Response Information Section').extension.where(url='http://hl7.org/fhir/us/ecr/StructureDefinition/rr-composition').valueIdentifier.where(use='official' and type.coding.code='88085-6').value",
"data_type": "string",
"nullable": true
},
"status": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Composition').section.where(title = 'Reportability Response Information Section').extension.where(url='http://hl7.org/fhir/us/ecr/StructureDefinition/rr-eicr-processing-status-extension').valueCodeableConcept.coding.where(system='urn:oid:2.16.840.1.114222.4.5.274').code",
"data_type": "string",
"nullable": true
},
"conditions": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.first().code='64572001' and code.coding.first().system='http://snomed.info/sct').valueCodeableConcept.coding.display",
"data_type": "string",
"nullable": true
},
"eicr_set_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition').identifier.where(type.coding.code = '55751-2').where(use='official').value",
"data_type": "string",
"nullable": true
},
"eicr_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition').id",
"data_type": "string",
"nullable": false
},
"eicr_version_number": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition' ).extension.where(url='http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber').valueString",
"data_type": "string",
"nullable": false
},
"replaced_eicr_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition').relatesTo.where(code='replaces').targetReference.reference",
"data_type": "string",
"nullable": true
},
"replaced_eicr_version": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition').relatesTo.where(code='replaces').extension.where(url='http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber').valueString",
"data_type": "string",
"nullable": true
},
"authoring_datetime": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Composition').date",
"data_type": "datetime",
"nullable": true
},
"provider_id": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Practitioner').where(extension.valueString='Responsible Party').identifier.value",
"data_type": "string",
"nullable": true
},
"facility_id_number": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Encounter')[0].location[0].id",
"data_type": "string",
"nullable": true
},
"facility_name": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Encounter')[0].location[0].location.display",
"data_type": "string",
"nullable": true
},
"facility_type": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Encounter')[0].location[0].extension.where(url = 'http://build.fhir.org/ig/HL7/case-reporting/StructureDefinition-us-ph-location-definitions.html#Location.type').valueCodeableConcept.coding[0].display",
"data_type": "string",
"nullable": true
},
"encounter_type": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Encounter')[0].class.where(system = 'urn:oid:2.16.840.1.113883.5.4').display",
"data_type": "string",
"nullable": true
},
"encounter_start_date": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Encounter').period.start",
"data_type": "datetime",
"nullable": true
},
"encounter_end_date": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Encounter').period.end",
"data_type": "datetime",
"nullable": true
},
"reason_for_visit": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition' ).section.where(code.coding.code='29299-5').extension.where(url='http://hl7.org/fhir/cda/ccda/StructureDefinition/2.16.840.1.113883.10.20.22.2.12').valueString",
"data_type": "string",
"nullable": true
},
"active_problems": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Condition').where(category.coding.code='problem-item-list')",
"data_type": "array",
"nullable": true,
"secondary_schema": {
"problem": {
"fhir_path": "Condition.code.coding.display",
"data_type": "string",
"nullable": true
},
"problem_date": {
"fhir_path": "Condition.onsetDateTime",
"data_type": "datetime",
"nullable": true
}
}
},
"labs": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')",
"data_type": "array",
"nullable": true,
"secondary_schema": {
"test_type": {
"fhir_path": "Observation.code.coding.display",
"data_type": "string",
"nullable": true
},
"test_type_code": {
"fhir_path": "Observation.code.coding.code",
"data_type": "string",
"nullable": true
},
"test_type_system": {
"fhir_path": "Observation.code.coding.system",
"data_type": "string",
"nullable": true
},
"test_result_qualitative": {
"fhir_path": "Observation.valueString",
"data_type": "string",
"nullable": true
},
"test_result_quantitative": {
"fhir_path": "Observation.valueQuantity.value",
"data_type": "float",
"nullable": true
},
"test_result_units": {
"fhir_path": "Observation.valueQuantity.unit",
"data_type": "string",
"nullable": true
},
"test_result_code": {
"fhir_path": "Observation.valueCodeableConcept.coding.code",
"data_type": "string",
"nullable": true
},
"test_result_code_display": {
"fhir_path": "Observation.valueCodeableConcept.coding.display",
"data_type": "string",
"nullable": true
},
"test_result_code_system": {
"fhir_path": "Observation.valueCodeableConcept.coding.system",
"data_type": "string",
"nullable": true
},
"test_result_interp": {
"fhir_path": "Observation.interpretation.coding.display",
"data_type": "string",
"nullable": true
},
"test_result_interp_code": {
"fhir_path": "Observation.interpretation.coding.code",
"data_type": "string",
"nullable": true
},
"test_result_interp_system": {
"fhir_path": "Observation.interpretation.coding.system",
"data_type": "string",
"nullable": true
},
"test_result_ref_range_low": {
"fhir_path": "Observation.refereneceRange.low.value",
"data_type": "float",
"nullable": true
},
"test_result_ref_range_low_units": {
"fhir_path": "Observation.refereneceRange.low.unit",
"data_type": "string",
"nullable": true
},
"test_result_ref_range_high": {
"fhir_path": "Observation.refereneceRange.high.value",
"data_type": "float",
"nullable": true
},
"test_result_ref_range_high_units": {
"fhir_path": "Observation.refereneceRange.high.unit",
"data_type": "string",
"nullable": true
},
"specimen_type": {
"fhir_path": "Observation.extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"data_type": "string",
"nullable": true
},
"performing_lab": {
"fhir_path": "Observation.performer.display",
"data_type": "string",
"nullable": true
},
"specimen_collection_date": {
"fhir_path": "Observation.extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"data_type": "datetime",
"nullable": true
}
}
},
"birth_sex": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http: //hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex').extension.value.coding.display",
"data_type": "string",
"nullable": true
},
"gender_identity": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http: //hl7.org/fhir/us/ecr/StructureDefinition/us-ph-genderidentity-extension').extension.value.coding.display",
"data_type": "string",
"nullable": true
},
"homelessness_status": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='75274-1').where(category.coding.code='social-history').valueCodeableConcept.coding.display",
"data_type": "string",
"nullable": true
},
"disabilities": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-disability-status').where(category.coding.code='social-history').where(valueBoolean).code.coding.display",
"data_type": "string",
"nullable": true
},
"tribal_affiliation": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http: //hl7.org/fhir/us/ecr/StructureDefinition/us-ph-tribal-affiliation-extension').extension.where(url='TribeName').value.display",
"data_type": "string",
"nullable": true
},
"tribal_enrollment_status": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http: //hl7.org/fhir/us/ecr/StructureDefinition/us-ph-tribal-affiliation-extension').extension.where(url='EnrolledTribeMember').value",
"data_type": "string",
"nullable": true
},
"current_job_title": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http://hl7.org/fhir/us/odh/StructureDefinition/odh-PastOrPresentJob').where(effectivePeriod.end.exists().not()).valueCodeableConcept.coding.display",
"data_type": "string",
"nullable": true
},
"current_job_industry": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http: //hl7.org/fhir/us/odh/StructureDefinition/odh-PastOrPresentJob').where(effectivePeriod.end.exists().not()).component.where(code.coding.code='86188-0').value.coding.display",
"data_type": "string",
"nullable": true
},
"usual_occupation": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http: //hl7.org/fhir/us/odh/StructureDefinition/odh-UsualWork').valueCodeableConcept.coding.display",
"data_type": "string",
"nullable": true
},
"usual_industry": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http: //hl7.org/fhir/us/odh/StructureDefinition/odh-UsualWork').component.where(code.coding.code='21844-6').value.coding.display",
"data_type": "string",
"nullable": true
},
"preferred_language": {
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Patient').communication.where(preferred).language.coding.display",
"data_type": "string",
"nullable": true
},
"pregnancy_status": {
"fhir_path": "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http: //hl7.org/fhir/us/ecr/StructureDefinition/us-ph-pregnancy-status-observation').value.coding.display",
"data_type": "string",
"nullable": true
}
}
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