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user [email protected] initiated a sync from Lightning
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@openfn @github-actions
openfn[bot] authored and github-actions[bot] committed Jun 13, 2024
1 parent 726ecca commit 08e6bcb
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229 changes: 151 additions & 78 deletions openfn-d52bd48e-451b-4a92-9aad-e7c62a7f0923-spec.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ name: jembi-demo
# credentials:
# globals:
workflows:
[Archive]-cdr-to-ndr:
name: [Archive] cdr-to-ndr
archive-cdr-to-ndr:
name: archive-cdr-to-ndr
jobs:
Map-and-process-data:
name: Map and process data
Expand Down Expand Up @@ -106,31 +106,31 @@ workflows:
target_job: Validate-with-NDR-HAPI-FHIR
condition_type: on_job_success
enabled: false
Map-and-process-data->Post-to-HAPI-FHIR:
source_job: Map-and-process-data
target_job: Post-to-HAPI-FHIR
condition_type: on_job_success
enabled: true
Post-to-HAPI-FHIR->Report-Error:
source_job: Post-to-HAPI-FHIR
target_job: Report-Error
condition_type: js_expression
condition_label: failed?
condition_expression: state.data.response.statusCode==400
enabled: true
Map-and-process-data->Post-to-HAPI-FHIR:
source_job: Map-and-process-data
target_job: Post-to-HAPI-FHIR
condition_type: on_job_success
enabled: true
cdr-to-ndr:
name: cdr-to-ndr
jobs:
Annonymize-Data:
name: Annonymize Data
Analyze-Data:
name: Analyze Data
adaptor: '@openfn/language-common@latest'
# credential:
# globals:
body: |
fn(state=> {
//Removig PII here before sending it to NDR
delete state.data.name;
delete state.data.telecom;
delete state.data.address;
delete state.data.contact;
delete state.data.extension; //contains religion, occupation, education level, target pop group
delete state.data.maritalStatus;
Expand All @@ -149,18 +149,24 @@ workflows:
// step. Click Docs to see list of operations or visit
// https://bit.ly/OFNJWG for our job writing guide
// and example job codes.
Create-Patient:
name: Create Patient
adaptor: '@openfn/language-fhir@latest'
create("Organization", $.organization)
Create-FHIR-Resource:
name: Create FHIR Resource
adaptor: '@openfn/language-http@latest'
# credential:
# globals:
body: |
// Use pure JavaScript to add operations to your
// step. Click Docs to see list of operations or visit
// https://bit.ly/OFNJWG for our job writing guide
// and example job codes.
post($.data.resourceType,
{
body: $.patient,
errors: { 400: false },
headers: {'content-type': 'application/json'},
parseAs: 'json'
},
state => {
state.data.response = state.response;
return state;
})
Create-Encounter:
name: Create Encounter
adaptor: '@openfn/language-fhir@latest'
Expand Down Expand Up @@ -189,95 +195,162 @@ workflows:
# credential:
# globals:
body: |
// Use pure JavaScript to add operations to your
// step. Click Docs to see list of operations or visit
// https://bit.ly/OFNJWG for our job writing guide
// and example job codes.
fn(state => {
state.errorLog = {
resource_id: state.data.id,
failure_type: 'validation error',
//data: state.references[0], //data we tried to create
resource_type: state.references[0].resourceType,
issue_code: state.data.issue[0].code,
issue_detail: state.data.issue[0].details.text,
issue_diagnostics: state.data.issue[0].diagnostics,
issue_location: state.data.issue[0].location,
last_updated: state.data.meta.lastUpdated,
statusCode: state.data.response.statusCode,
statusMessage: state.data.response.statusMessage
}
console.log('Error to log:: ', JSON.stringify(state.errorLog,null,2));
return state;
});
// insert('fhir_errors',
// state => state.errorLog,
// { logValues: true }
// );
//kafka mappings - don't think we need these
// ts: state.request.ts,
// topic: state.request.topic,
// offset: state.request.offset,
// partition: state.request.partition,
// key: state.request.key,
Map-Data:
name: Map Data
adaptor: '@openfn/language-common@latest'
# credential:
# globals:
body: |
fn(state=> {
const fhirData = state.data;
const patient = {
resourceType: fhirData.resourceType,
id: fhirData.id,
identifier: fhirData.identifier.map(id => ({
system: id.system,
value: id.value,
})),
active: fhirData.active,
gender: fhirData.gender,
birthDate: fhirData.birthDate,
//Map CDR data to NDR FHIR IG
const cdrData = state.data;
const patient = {
resourceType: cdrData.resourceType,
id: cdrData.id,
identifier: cdrData.identifier.map(id => ({
type: id.system == "http://cdr.aacahb.gov.et/MRN"? {
"coding": [
{
"code": "MR",
"display": "Medical record number",
"system": "http://terminology.hl7.org/CodeSystem/v2-0203"
}
],
"text": "Medical record number"
} : undefined,
system: id.system,
value: id.value,
})),
active: cdrData.active,
gender: cdrData.gender,
birthDate: cdrData.birthDate,
address: cdrData.address,
managingOrganization: cdrData.managingOrganization,
deceasedBoolean: cdrData.deceasedBoolean,
text: cdrData.text
};
// returned the mapped patient object
return {...state, patient}
})
Remove-PIIs:
name: Remove PIIs
adaptor: '@openfn/language-common@latest'
# credential:
# globals:
body: |
fn(state=> {
//Removig PII here before sending it to NDR
delete state.data.name;
delete state.data.telecom;
delete state.data.contact;
delete state.data.extension; //contains religion, occupation, education level, target pop group
delete state.data.maritalStatus;
managingOrganization: fhirData.managingOrganization.reference,
deceasedBoolean: fhirData.deceasedBoolean,
text: fhirData.text
};
//only keeping birthdate and gender
return {...state, patient}
return state;
})
triggers:
webhook:
type: webhook
enabled: true
edges:
webhook->Annonymize-Data:
webhook->Analyze-Data:
source_trigger: webhook
target_job: Annonymize-Data
target_job: Analyze-Data
condition_type: always
enabled: true
Create-Encounter->Log-error:
source_job: Create-Encounter
target_job: Log-error
condition_type: on_job_failure
enabled: true
Create-Condition->Log-error:
source_job: Create-Condition
target_job: Log-error
condition_type: on_job_failure
enabled: true
Create-Patient->Log-error:
source_job: Create-Patient
target_job: Log-error
condition_type: on_job_failure
enabled: true
Create-Organization->Log-error:
source_job: Create-Organization
Create-FHIR-Resource->Log-error:
source_job: Create-FHIR-Resource
target_job: Log-error
condition_type: on_job_failure
enabled: true
Annonymize-Data->Map-Data:
source_job: Annonymize-Data
target_job: Map-Data
condition_type: on_job_success
enabled: true
Map-Data->Create-Organization:
source_job: Map-Data
target_job: Create-Organization
condition_type: on_job_success
condition_type: js_expression
condition_label: failed?
condition_expression: state.data.response.statusCode==400
enabled: true
Map-Data->Create-Condition:
Map-Data->Create-FHIR-Resource:
source_job: Map-Data
target_job: Create-Condition
target_job: Create-FHIR-Resource
condition_type: on_job_success
enabled: true
Map-Data->Create-Patient:
source_job: Map-Data
target_job: Create-Patient
Analyze-Data->Remove-PIIs:
source_job: Analyze-Data
target_job: Remove-PIIs
condition_type: on_job_success
enabled: true
Map-Data->Create-Encounter:
source_job: Map-Data
target_job: Create-Encounter
Remove-PIIs->Map-Data:
source_job: Remove-PIIs
target_job: Map-Data
condition_type: on_job_success
enabled: true
test-patient-fhir:
name: test-patient-fhir
jobs:
parse-json:
name: parse json
adaptor: '@openfn/language-common@latest'
# credential:
# globals:
body: |
fn(state => {
const parsedData = JSON.parse(state.data.body);
console.log(parsedData);
state.resource = parsedData.entry[0].resource;
console.log('show only the resource:: ', state.resource);
return state;
})
//testing using create instead of post
//create("Patient", state => state.data)
//headers: {'content-type': 'application/json'},
//errors: { 400: false },
//parseAs: 'json',
// , state => {
// //console.log('response ::', JSON.stringify(state.response, null,2));
// state.data.response = state.response;
// return state;
// }
triggers:
webhook:
type: webhook
enabled: true
edges:
webhook->parse-json:
source_trigger: webhook
target_job: parse-json
condition_type: always
enabled: true
test-patient-http:
name: test-patient-http
jobs:
Post-Patient:
name: Post Patient
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