function translateLabsFhir(chcsLabResultObjectModified, _options, prefix) {
// Assign the default options, then override what the caller wants. At the end you have the right options.
var options = {
warnings: false,
policy: false,
eat: true
};
for (k in _options) {
if (_options.hasOwnProperty(k)) options[k] = _options[k];
}
var participatingProperties = []; // no participants yet
var warnings = []; // no warnings yet
// Create a fetcher for chcsLabResultObject. The fetcher will get data values from
// input chcsLabResultObject, remembering those that actually have values in list participating_properties.
// var fetch1 = fdt.peek(chcsLabResultObjectModified, participatingProperties);
var peek = fdt.peek(chcsLabResultObjectModified, participatingProperties);
var eat = fdt.eat(chcsLabResultObjectModified, participatingProperties);
eat('$.type');
// fetch1(json_pattern[, transformation])
var identifier = eat('$.type', function (t) { return [ fdt.fhirIdentifier(t) ]; }); // Identifier Id for external references to this report
var patient = chcsLabResultObjectModified['patient-63'];
// "internal" conversion functions, if a key is present then its values are an array of
// tests of that type.
// "micro_conversion_flag-63"
function micro_conversion(mc) {
}
// "blood_bank-63"
function blood_bank(bb) {
}
// "clinical_chemistry-63"
function clinical_chemistry(cc) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['ch'], text: "Chemistry"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: patient, // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [cc] // Attachment , Entire report as issued
});
}
// "parasitology_buffer-63", https://en.wikipedia.org/wiki/Parasitology
function parasitology_buffer(pb) {
// details tbs
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['par'], text: "Parasitology"}, // deprecated, CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: rdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [pb] // Attachment , Entire report as issued
});
}
// "bacteriology_buffer-63"
function bacteriology_buffer(bb) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [bb] // Attachment , Entire report as issued
});
}
// "mycobacterium_buffer-63"
function mycobacterium_buffer(mb) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['mcb'], text: "Mycobacteriology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [mb] // Attachment , Entire report as issued
});
}
// "mycology_buffer-63"
function mycology_buffer(mb) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['myc'], text: "Mycology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [mb] // Attachment , Entire report as issued
});
}
// "virology_buffer-63"
function virology_buffer(vb) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['vr'], text: "Virology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [vb] // Attachment , Entire report as issued
});
}
// "delta_check-63", http://www.medilexicon.com/medicaldictionary.php?t=23464
function delta_check(dc) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [dc] // Attachment , Entire report as issued
});
}
// "surgical_pathology-63"
function surgical_pathology(sp) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['sp'], text: "Surgical Pathology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [sp] // Attachment , Entire report as issued
});
}
// "cytology_gyn-63"
function cytology_gyn(cg) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['cy'], text: "Cytogenetics"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [cg] // Attachment , Entire report as issued
});
}
// "autopsy-63"
function autopsy(a) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [a] // Attachment , Entire report as issued
});
}
// "bone_marrow-63"
function bone_marrow(bm) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [bm] // Attachment , Entire report as issued
});
}
// "cytology_nongyn-63"
function cytology_nongyn(cn) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [cn] // Attachment , Entire report as issued
});
}
// "parasitology-63"
function parasitology(p) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['par'], text: "Parasitology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [p] // Attachment , Entire report as issued
});
}
// "bacteriology-63"
function bacteriology(b) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['oth'], text: "Other"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [b] // Attachment , Entire report as issued
});
}
// "mycobacterium-63"
function mycobacterium(m) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['mcb'], text: "Mycobacteriology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [m] // Attachment , Entire report as issued
});
}
// "mycology-63"
function mycology(m) {
return fdt.clean({
resourceType: "DiagnosticReport",
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['myc'], text: "Mycology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [m] // Attachment , Entire report as issued
});
}
// "virology-63"
function virology(v) {
return fdt.clean({
resourceType: "DiagnosticReport",
id: fdt.fhirId(resourceType, eat('$._id')),
// from Resource: id, meta, implicitRules, and language
identifier: identifier,
// from DomainResource: text, contained, extension, and modifierExtension
status: fdt.required({coding: ["final"]}), // R! registered | partial | final | corrected | appended | cancelled | entered-in-error
category: {coding: ['vr'], text: "Virology"}, // CodeableConcept, Service category, http://hl7-fhir.github.io/valueset-diagnostic-service-sections.html
code: fdt.required({}), // R! Name/Code for this diagnostic report, loinc http://hl7-fhir.github.io/valueset-report-codes.html
subject: fdt.required(patient), // Reference(Patient|Group|Device|Location) R! The subject of the report, usually, but not always, the patient
encounter: {}, // Reference(Encounter) Health care event when test ordered
// effective[x]: Clinically Relevant time/time-period for report. One of these 2:
effectiveDateTime: "<dateTime>",
effectivePeriod: {}, // Period
issued: fdt.required("<instant>"), // R! DateTime this version was released
performer: fdt.required({}), // Reference(Practitioner|Organization) R! Responsible Diagnostic Service
request: [{}], // Reference(DiagnosticOrder|ProcedureRequest|ReferralRequest) What was requested
specimen: [{}], // Reference(Specimen) Specimens this report is based on
result: [{}], // Reference(Observation) Observations - simple, or complex nested groups
imagingStudy: [{}], // Reference(ImagingStudy|ImagingObjectSelection) Reference to full details of imaging associated with the diagnostic report
image: [{ // Key images associated with this report
comment: "<string>", // Comment about the image (e.g. explanation)
link: fdt.required({}) // Reference(Media) R! Reference to the image source
}],
conclusion: "<string>", // Clinical Interpretation of test results
codedDiagnosis: [{}], // CodeableConcept , Codes for the conclusion
presentedForm: [c] // Attachment , Entire report as issued
});
}
var labKinds = [micro_conversion, blood_bank, clinical_chemistry,
parasitology_buffer, bacteriology_buffer, mycobacterium_buffer, mycology_buffer,
virology_buffer, delta_check, surgical_pathology, cytology_gyn,
autopsy, bone_marrow, cytology_nongyn, parasitology, bacteriology,
mycobacterium, mycology, virology];
var fhirDiagnosticReports = [];
// Take the cross product of all lab kinds, labKinds by their appearances in a Lab_Reports-63 object and
// push their translations onto fhirDiagnosticReports.
labKinds.forEach(function(lk) {
eat("$." + lk.name + '-63', function (l) {
if (l) l.forEach(function(i) {
fhirDiagnosticReports.push(lk(i));
});
});
});
if (options.participants) fhir.addParticipants(fhirDiagnosticReports, participatingProperties, prefix);
if (options.warnings) fhir.addWarnings(fhirDiagnosticReports, warnings);
fdt.clean(fhirDiagnosticReports);
// Additional semantic processing here
// var used = new Av();
// participatingProperties.forEach(function (p) {
// var prop = p.substring(1);
// eval('used' + prop + '= chcsLabResultObjectModified' + prop);
// });
// var object_used = chcs_utils.devivify(used);
//
// if (options.eat) {
// participatingProperties.forEach(function(p){
// var prop = p.substring(1);
// eval('delete chcsLabResultObjectModified' + prop);
// });
// }
return {
// used: object_used,
fhir: fhirDiagnosticReports,
participants: participatingProperties,
options: options
};
}
function translatePrescriptionsFhir(chcsPrescriptionObjectModified, _options, prefix) {
// Assign the default options, then override what the caller wants. At the end you have the right options.
var options = {
warnings: false,
policy: false,
eat: true
};
for (k in _options) {
// istanbul ignore else
if (_options.hasOwnProperty(k)) { options[k] = _options[k]; }
}
// var participatingProperties = ["$['type']"]; // no participants yet
var participatingProperties = []; // no participants yet
// Create a fetcher for chcsPrescriptionObject. The fetcher will get data values from
// input chcsPrescriptionObject, remembering those that actually have values in list participatingProperties.
// var fetch1 = fdt.peek(chcsPrescriptionObjectModified, participatingProperties); // => fetch1(json_pattern[, transformation])
var peek = fdt.peek(chcsPrescriptionObjectModified, participatingProperties); // => fetch1(json_pattern[, transformation])
var eat = fdt.eat(chcsPrescriptionObjectModified, participatingProperties); // => fetch1(json_pattern[, transformation])
eat('$.type');
var warnings = []; // no warnings yet
// http://hl7-fhir.github.io/medication.html:
// "This resource is primarily used for the identification and definition of a medication. It covers the ingredients
// and the packaging for a medication."
// http://hl7-fhir.github.io/medicationdispense.html:
// "Indicates that a medication product is to be or has been dispensed for a named person/patient. This includes a
// description of the medication product (supply) provided and the instructions for administering the medication.
// The medication dispense is the result of a pharmacy system responding to a medication order."
var resourceType = 'MedicationDispense';
// var whenPrepared = fetch1('$.fill_dates-52[0].fill_dates-52_01.value');
var whenPrepared = eat('$.login_date-52.value');
var fhirMedication = {
resourceType: resourceType,
id: fdt.fhirId(resourceType, peek('$._id')),
// from Resource: id, meta, implicitRules, and language
// from DomainResource: text, contained, extension, and modifierExtension
identifier: eat('$._id', function(i) { return fdt.fhirExternalIdentifier(i, 'Prescription'); }),
status: 'completed', // in-progress | on-hold | completed | entered-in-error | stopped, NOT MAPPED
// medication[x]: What medication was supplied. One of these 2:
medicationCodeableConcept: eat('$.drug-52.label', fdt.fhirCodeableConcept), // Reference(Medication)
medicationReference: eat('$.drug-52', fdt.fhirReferenceMedication), // Reference(Medication)
patient: eat('$.patient-52', fdt.fhirReferencePatient),
dispenser: eat('$.provider-52', fdt.fhirReferencePractioner), // Reference(Practitioner), Practitioner responsible for dispensing medication
authorizingPrescription: eat('order_pointer-52', function (p) { return [ fdt.fhirReferenceMedicationOrder(p) ]; }), // Medication order that authorizes the dispense, TODO: cross ref?
// type: fetch1("$.type", fhirCodeableConcept), // Trial fill, partial fill, emergency fill, etc., NOT FOUND
quantity: eat('$.qty-52', fdt.fhirQuantity), // { Quantity(SimpleQuantity) }, // Amount dispensed
daysSupply: eat('$.days_supply-52', fdt.fhirQuantity), // { Quantity(SimpleQuantity) }, // Amount of medication expressed as a timing amount
whenPrepared: whenPrepared, // Dispense processing time
whenHandedOver: whenPrepared, // When product was given out
destination: eat('$.outpatient_site-52', fdt.ReferenceLocation), // Where the medication was sent
// receiver: [{ Reference(Patient|Practitioner) }], // Who collected the medication
note: eat('$.comments-52', function(c) { return [{ text: c }]; }), // Information about the dispense
dosageInstruction: [ // Medicine administration instructions to the patient/caregiver
{
text: peek('$.sig-52', function(t) { return encoder.htmlEncode(t); }), // "text" : "<string>", // Free text dosage instructions e.g. SIG
additionalInstructions: eat('$.expanded_sig-52', function(ai) { return fdt.fhirCodeableConcept(encoder.htmlEncode(ai)); }), // E.g. "Take with food"
timing: eat('$.sig-52', function(sig) {return fdt.fhirTiming(encoder.htmlEncode(sig), whenPrepared); }), // When medication should be administered
// // asNeeded[x]: Take "as needed" f(or x). One of these 2:
// asNeededBoolean: fetch1('$.expanded_sig-52', function(s) { return s.match(/as needed/i); }), // "asNeededBoolean" : <boolean>,
asNeededBoolean: eat('$.expanded_sig-52', function(s) { return s.match(/as needed/i) ? true : false; }), // "asNeededBoolean" : <boolean>,
// "asNeededCodeableConcept" : { CodeableConcept },
// site[x]: Body site to administer to. One of these 2:
// "siteCodeableConcept" : { CodeableConcept },
// "siteReference" : { Reference(BodySite) },
// "route" : { CodeableConcept }, // How drug should enter body
// "method" : { CodeableConcept }, // Technique for administering medication
// dose[x]: Amount of medication per dose. One of these 2:
// "doseRange" : { Range },
// "doseQuantity" : { Quantity(SimpleQuantity) },
// rate[x]: Amount of medication per unit of time. One of these 2:// "rateRatio" : { Ratio },
// "rateRange" : { Range },
// "maxDosePerPeriod" : { Ratio } // Upper limit on medication per unit of time
}],
// substitution: { // Deals with substitution of one medicine for another
// R! Code signifying whether a different drug was dispensed from what was prescribed
// reason: [{CodeableConcept}], // Why was substitution made
// responsibleParty: [{Reference(Practitioner)}] // Who is responsible for the substitution
};
// istanbul ignore if
if (options.participants) fhir.addParticipants(fhirMedication, participatingProperties, prefix);
// istanbul ignore if
if (options.warnings) fhir.addWarnings(fhirMedication, warnings);
// Remove keys that have undefined/null/[] values.
fdt.clean(fhirMedication);
// The FHIR spec indicates that well-formed MedicationDispenses are required to have one of these two values.
// Generally the medicationReference will be the key that's populated.
// istanbul ignore if
if (options.policy && !_.has(fhirMedication, 'medicationReference') && !_.has(fhirMedication, 'medicationCodeableConcept')) {
throw new Error(format("FHIR medication '{id}' contains neither a medicationReference nor a medicationCodeableConcept.", {id: fhirMedication.value}));
}
// var used = new Av(); // {};
// participatingProperties.forEach(function (p) {
// var prop = p.substring(1);
// eval('used' + prop + '= chcsPrescriptionObjectModified' + prop);
// });
// var object_used = chcs_utils.devivify(used);
//
// if (options.eat) {
// participatingProperties.forEach(function(p){
// var prop = p.substring(1);
// eval('delete chcsPrescriptionObjectModified' + prop);
// });
// }
return {
// used: object_used,
options: options,
participants: participatingProperties,
fhir: fhirMedication
};
}
/**
* Translate a chcsPrescriptionObject into a fhir_MedicationDispense.
* @param {object} chcsPrescriptionObject -- input object
* @param {{policy: boolean, warnings: boolean, eat: boolean}} [_options={policy: false, warnings: false, eat: true}]
* @returns {object} -- fhir translation, a MedicationDispense resource
* @see {@link http://hl7-fhir.github.io/procedure.html}
*/
function translateProceduresFhir(chcsProcedureObjectModified, _options, prefix) {
// Assign the default options, then override what the caller wants. At the end you have the right options.
var options = {
participants: false,
warnings: false,
policy: false,
eat: true
};
for (k in _options) {
if (_options.hasOwnProperty(k)) {
options[k] = _options[k];
}
}
var participatingProperties = []; // no participants yet
var warnings = []; // no warnings yet
// Create a fetcher for chcsProcedureObject. The fetcher will get data values from
// input chcsProcedureObject, remembering those that actually have values in list participating_properties.
// var fetch1 = fdt.peek(chcsProcedureObjectModified, participatingProperties); // returns function fetch1(json_pattern[, transformation])
var peek = fdt.peek(chcsProcedureObjectModified, participatingProperties); // returns function fetch1(json_pattern[, transformation])
var eat = fdt.eat(chcsProcedureObjectModified, participatingProperties); // returns function fetch1(json_pattern[, transformation])
eat('$.type');
// http://hl7-fhir.github.io/procedure.html:
// "This resource is used to record the details of procedures performed on a patient. A procedure is an activity
// that is performed with or on a patient as part of the provision of care. Examples include surgical procedures,
// diagnostic procedures, endoscopic procedures, biopsies, counseling, physiotherapy, exercise, etc.
// Procedures may be performed by a healthcare professional, a friend or relative or in some cases
// by the patient themselves."
var resourceType = 'Procedure';
// TODO mike@carif.io: the 'Patient-' prefix breaks with the chcs naming conventions. Check this.
var thePatient = eat('$.patient.id', function(p) { return '2-' + p.substring('Patient-'.length); });
var theProcedure = eat('$._id', function(p) { return p.substring('Procedure-'.length); });
var theLabel = eat('$.patient.label');
var fhirProcedure = {
resourceType: resourceType,
id: fdt.fhirId(resourceType, eat('$._id')),
// from Resource: id, meta, implicitRules, and language
// from DomainResource: text, contained, extension, and modifierExtension
identifier: theProcedure && fdt.fhirIdentifierList(theProcedure, 'Procedure'), // External Identifiers for this procedure
subject: thePatient && theLabel && fdt.fhirReferencePatient({id: thePatient, label: theLabel}), // { Reference(Patient|Group) }, // R! Who the procedure was performed on
status: 'completed', // R! in-progress | aborted | completed | entered-in-error
category: peek('$.source.id', fdt.fhirCodeableConcept), // { CodeableConcept }, // Classification of the procedure
code: eat('$.source.id', fdt.fhirCodeableConcept), // { CodeableConcept }, // R! Identification of the procedure
// notPerformed: false, // <boolean>, // True if procedure was not performed as scheduled
// reasonNotPerformed: // [{ CodeableConcept }], // C? Reason procedure was not performed
// bodySite: fetch1('', fdt.fhirCodeableConcept), // [{ CodeableConcept }], // Target body sites
// reason[x]: Reason procedure performed. One of these 2:
// reasonCodeableConcept: fetch1('', fdt.fhirCodeableConcept), // { CodeableConcept },
// "reasonReference" : { Reference(Condition) },
// performer: fetch1('$.provider', function (p) {
// return [{ // The people who performed the procedure
// actor: fdt.fhirReferencePractioner(p.id), // { Reference(Practitioner|Organization|Patient|RelatedPerson) }, // The reference to the practitioner
// role: fdt.fhirCodeableConcept(p) // { CodeableConcept } // The role the actor was in
// }];
// }),
// // performed[x]: Date/Period the procedure was performed. One of these 2:
performedDateTime: eat('$.dateReported.value'), // "<dateTime>",
// "performedPeriod" : { Period },
encounter: eat('$.comments', function (e) { return { display: e }; }), // The encounter associated with the procedure
// location: fetch1('', fdt.fhirReferenceLocation), // { Reference(Location) }, // Where the procedure happened
// outcome: fetch1('', fdt.fhirCodeableConcept), // { CodeableConcept }, // The result of procedure
// report: fetch1('', function (r) { return [ producingThisDiagnosticReport || fdt.ReferenceDiagnosticReport(r) ]; }), // { Reference(DiagnosticReport) }], // Any report resulting from the procedure
// complication: fetch1('', fdt.CodeableConceptList), // Complication following the procedure
// followUp: fetch1('', fdt.CodeableConceptList), // Instructions for follow up
// "request" : { Reference(CarePlan|DiagnosticOrder|ProcedureRequest|ReferralRequest) }, // A request for this procedure
// notes: fetch1('', function(a) { return [a]; }), // [{ Annotation }], // Additional information about the procedure
// "focalDevice" : [{ // Device changed in procedure
// "action" : { CodeableConcept }, // Kind of change to device
// "manipulated" : { Reference(Device) } // R! Device that was changed
// }],
//"used" : [{ Reference(Device|Medication|Substance) }] // Items used during procedure
};
if (options.participants) fhir.addParticipants(fhirProcedure, participatingProperties, prefix);
if (options.warnings) fhir.addWarnings(fhirProcedure, warnings);
// Remove keys that have undefined/null/[] values.
fdt.clean(fhirProcedure);
// Additional semantic processing here
// var used = new Av();
// participatingProperties.forEach(function (p) {
// var prop = p.substring(1);
// eval('used' + prop + '= chcsProcedureObjectModified' + prop);
// });
//
// if (options.eat) {
// participatingProperties.forEach(function(p){
// var prop = p.substring(1);
// eval('delete chcsProcedureObjectModified' + prop);
// });
// }
// var object_used = chcs_utils.devivify(used);
//
return {
// used: object_used,
fhir: fhirProcedure,
participants: participatingProperties,
options: options
};
}