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Implement saving and loading of externalID #68

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Implement saving and loading of externalID #68

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9836993
Implement saving and loading of externalID
shermanlo77 May 12, 2023
017b886
Rename externalID to identifier in patientResource
shermanlo77 Jan 10, 2024
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19 changes: 17 additions & 2 deletions src/script/GA4GHFHIRConverter.js
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Original file line number Diff line number Diff line change
Expand Up @@ -474,9 +474,9 @@ GA4GHFHIRConverter.extractDataFromObservation = function (observationResource, n
let nodeData = nodeDataLookup[familyMember];

let fhirTerminologyHelper = editor.getFhirTerminologyHelper();

let foundCode = false;

if (observationResource.valueCodeableConcept) {
for (const coding of observationResource.valueCodeableConcept.coding) {
if (coding.system === 'http://snomed.info/sct' && coding.code === '87955000') {
Expand Down Expand Up @@ -603,6 +603,13 @@ GA4GHFHIRConverter.extractDataFromPatient = function (patientResource,
properties.gender = 'F';
}

if (patientResource.identifier) {
if (patientResource.identifier.system ===
'https://github.com/phenotips/open-pedigree?externalID') {
properties.externalID = patientResource.identifier.value;
}
}

const dateTimeSplitter = /([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)(\.[0-9]+)?(Z|(\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00)))?)?)?/;
const nameUseOrder = ['anonymous', 'temp', 'expired_nickname', 'expired_', 'expired_usual', 'expired_official', 'maiden', 'old', 'nickname', '', 'usual', 'official'];
let maxFNameUse = -2;
Expand Down Expand Up @@ -1281,6 +1288,14 @@ GA4GHFHIRConverter.buildPedigreeIndividual = function (containedId, nodeProperti
}
}
}

if (nodeProperties.externalID) {
patientResource.identifier = {
'system': 'https://github.com/phenotips/open-pedigree?externalID',
'value': nodeProperties.externalID
};
}

return patientResource;
};

Expand Down