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FHIR terminology import #2610

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FHIR terminology import #2610

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b99b3b5
Initial implementation of FHIR value set import
johngrimes Aug 25, 2021
9fe7b3c
Merge remote-tracking branch 'origin/master' into fhir-import
johngrimes Sep 6, 2021
4b5fe4c
Move terminology server URL out to config, and set Accept header
johngrimes Sep 6, 2021
1b07a3a
Merge remote-tracking branch 'ohdsi/master' into fhir-import
johngrimes Feb 8, 2022
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9 changes: 8 additions & 1 deletion js/components/conceptset/import.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ define([
'./import/identifiers',
'./import/sourcecodes',
'./import/conceptset',
'./import/fhir',
],function(
ko,
view,
Expand Down Expand Up @@ -60,6 +61,12 @@ define([
{
title: ko.i18n('components.conceptSet.repository', 'Repository'),
key: 'repository',
},
{
title: ko.i18n('components.conceptSet.fhir', 'FHIR'),
key: 'fhir',
componentName: 'conceptset-list-import-fhir',
componentParams: {...params, appendConcepts: this.appendConcepts}
}
];
}
Expand Down Expand Up @@ -125,4 +132,4 @@ define([
}

return commonUtils.build('conceptset-list-import', ConceptSetImport, view);
});
});
18 changes: 18 additions & 0 deletions js/components/conceptset/import/fhir.html
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@@ -0,0 +1,18 @@
<div>
<div class="heading">
<span data-bind="text: ko.i18n('components.conceptSet.fhirHeading', 'Import a value set from a FHIR terminology server')"></span>
</div>
<label>
<span data-bind="text: ko.i18n('components.conceptSet.fhirServer', 'FHIR server URL')"></span>
<input class="form-control" type="text" name="fhirServer" data-bind="textInput: fhirServer"/>
</label>
<label>
<span data-bind="text: ko.i18n('components.conceptSet.valueSet', 'Value set URI')"></span>
<input class="form-control" type="text" name="valueSet" data-bind="textInput: valueSet"/>
</label>
<concept-add-box params="{
isActive: canAddConcepts,
onSubmit: doImport,
}"></concept-add-box>
<div class="clear"></div>
</div>
51 changes: 51 additions & 0 deletions js/components/conceptset/import/fhir.js
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@@ -0,0 +1,51 @@
define([
'knockout',
'text!./fhir.html',
'components/Component',
'./ImportComponent',
'utils/AutoBind',
'utils/Clipboard',
'utils/CommonUtils',
'services/VocabularyProvider',
'services/http',
'appConfig',
], function(
ko,
view,
Component,
ImportComponent,
AutoBind,
Clipboard,
commonUtils,
vocabularyApi,
httpService,
config
){

class FhirImport extends AutoBind(ImportComponent(Component)) {
constructor(params) {
super(params);
this.fhirServer = ko.observable(config.fhirTerminologyUrl);
this.valueSet = ko.observable("");
this.appendConcepts = params.appendConcepts;
this.canAddConcepts = ko.pureComputed(() =>
this.fhirServer().length > 0 &&
this.valueSet().length > 0 &&
params.canEdit()
);
this.doImport = this.doImport.bind(this);
}

async runImport(options) {
const expandUrl = `${this.fhirServer()}/ValueSet/$expand`,
expandParams = {
url: this.valueSet()
}, result = await httpService.fhirService.doGet(expandUrl, expandParams),
codes = result.data.expansion.contains.map(c => c.code),
{data} = await vocabularyApi.getConceptsByCode(codes);
this.appendConcepts(data, options);
}
}

return commonUtils.build('conceptset-list-import-fhir', FhirImport, view);
});
2 changes: 2 additions & 0 deletions js/config/app.js
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Expand Up @@ -151,5 +151,7 @@ define(function () {
}
};

appConfig.fhirTerminologyUrl = "https://r4.ontoserver.csiro.au/fhir";

return appConfig;
});
17 changes: 16 additions & 1 deletion js/services/http.js
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Expand Up @@ -3,7 +3,7 @@ define(function(require, exports) {
const config = require('appConfig');
const sharedState = require('atlas-state');
const { Api:OHDSIApi, STATUS } = require('ohdsi-api');
const JSON_RESPONSE_TYPE = 'application/json';
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This looks like it replaced JSON_RESPONSE_TYPE with FHIR_JSON_RESPONSE_TYPE, and I don't think you should remove JSON_RESPONSE_TYPE...can you confirm?

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I was also curious about this change and it looks like JSON_RESPONSE_TYPE is already defined in the base class here: https://github.com/OHDSI/UiToolbox/blob/master/src/api/index.js#L15. So I think it is safe to remove.

const FHIR_JSON_RESPONSE_TYPE = 'application/fhir+json';
const TEXT_RESPONSE_TYPE = 'text/plain';
const EventBus = require('services/EventBus');

Expand Down Expand Up @@ -100,6 +100,18 @@ define(function(require, exports) {
}
}

class FhirApi extends Api {
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I don't think FhirApi should be a nested class in http.js. The http.js is a module which facilitates http communication. I think the FHIR class handles communicating to a FHIR service. We have a separate folder of services which you can implement your class there, and then you can import the class in the javascript compoennt you want to use (via the define())

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FYI: within this file we do define 2 classes: Api and PlainTextApi. I agree with moving this to another file but noting that we may want to do that for the PlainTextApi as well.

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Apologies, my understanding about the http.js module was that it just wrapped some lower-level HTTP calls to handle passing specific headers, but not something that made some kind of 'client api' to a specific type of service (like the FHIR one or the PlainText one)...I'm not sure what the design decision was about introducing the PlainText api into http.js but it seems that whoever put that forward thought that you would put these type of API clients directly into the http.js module...so, I can't argue with that, so my only comment then is how the JSON_RESPONSE_TYPE was removed....although not sure where that is being used (but possibly it's a constant that is refernced elsewhere in the app).

getHeaders(requestUrl) {
return {
'Accept': FHIR_JSON_RESPONSE_TYPE,
};
}

parseResponse(json) {
return JSON.parse(json);
}
}

const singletonApi = new Api();
singletonApi.setAuthTokenHeader('Authorization');

Expand All @@ -108,7 +120,10 @@ define(function(require, exports) {
plainTextService.setUnauthorizedHandler(() => singletonApi.handleUnauthorized());
plainTextService.setUserTokenGetter(() => singletonApi.getUserToken());

const fhirService = new FhirApi();

singletonApi.plainTextService = plainTextService;
singletonApi.fhirService = fhirService;

return singletonApi;
});