Latest changes from staging (#11)

* [skip actions] Configure OpenFn * Update second workflow (#5) * add program * code format * wip: update mappings for create encounter * cereate-events * Update workflow file path * remove ocl mapping * Changes accepted by Lightning; updated current project state * Update 4-get-options-map.js add missing mapping * Changes accepted by Lightning; updated current project state * dataValue mapping- return option code not option uid * Changes accepted by Lightning; updated current project state * add identifier mappings * add draft mappings for other TEAs for wf2 * updating identifier mapping, draft mappings for other TEAs * cleaning up comments * mapping fixes per testing * update gist url * update mhpss mappings with question names * update transformation logic Ref #2 improvements * Update 4-get-options-map.js * Update 4-get-options-map.js * Update 4-get-options-map.js * user [email protected] initiated a sync from Lightning * add back config.json file * Changes accepted by Lightning; updated current project state * user [email protected] initiated a sync from Lightning --------- Co-authored-by: mtuchi <[email protected]> Co-authored-by: Aleksa Krolls <[email protected]> Co-authored-by: aleksa-krolls <[email protected]> Co-authored-by: aleksa-krolls <[email protected]> Co-authored-by: openfn[bot] <openfn[bot]@users.noreply.github.com>
OpenFn · Sep 11, 2024 · 739077a · 739077a
1 parent 2e69404
commit 739077a
Show file tree

Hide file tree

Showing 14 changed files with 947 additions and 254 deletions.
diff --git a/.github/workflows/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-deploy.yml b/.github/workflows/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-deploy.yml
@@ -0,0 +1,21 @@
+on:
+  push:
+    branches:
+      - staging
+
+concurrency:
+  group: openfn-deployment
+  cancel-in-progress: false
+
+jobs:
+  deploy-to-lightning:
+    runs-on: ubuntu-latest
+    name: A job to deploy to Lightning
+    permissions:
+      contents: write
+    steps:
+      - name: openfn deploy
+        uses: openfn/[email protected]
+        with:
+          secret_input: ${{ secrets.OPENFN_cd92dd57_9a3c_4318_bdcb_f57a386cf811_API_KEY }}
+          config_path_input: 'openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-config.json'
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+jsconfig.json
 # temp
 tmp
 

diff --git a/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-config.json b/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-config.json
@@ -0,0 +1,5 @@
+{
+    "endpoint": "https://app.openfn.org",
+    "specPath": "openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-spec.yaml",
+    "statePath": "openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-state.json"
+}
diff --git a/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-spec.yaml b/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-spec.yaml
diff --git a/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-state.json b/openfn-cd92dd57-9a3c-4318-bdcb-f57a386cf811-state.json
diff --git a/workflows/wf2/1-get-patients.js b/workflows/wf2/1-get-patients.js
@@ -13,18 +13,18 @@ fn(state => {
   return state;
 });
 
-searchPatient({ q: 'Patient', v: 'full', limit: '100' });
+searchPatient({ q: 'Aisha', v: 'full', limit: '3' });
+// searchPatient({ q: 'Patient', v: 'full', limit: '100' });
 //Query all patients (q=all) not supported on demo OpenMRS; needs to be configured
 //...so we query all Patients with name "Patient" instead
 
 fn(state => {
   const { results } = state.data;
 
-  const getPatientByUuid = uuid => {
-    return results.find(patient => patient.uuid === uuid);
-  };
-  // console.log('dateCreated for patient uuid ...2c6dbfc5acc8',getPatientByUuid("31b4d9c8-f7cc-4c26-ae61-2c6dbfc5acc8").auditInfo.dateCreated)
+  const getPatientByUuid = uuid =>
+    results.find(patient => patient.uuid === uuid).auditInfo.dateCreated;
 
+  // console.log('dateCreated for patient uuid ...2c6dbfc5acc8',getPatientByUuid("31b4d9c8-f7cc-4c26-ae61-2c6dbfc5acc8"))
   //console.log(JSON.stringify(state.data, null, 2));
 
   console.log('Filtering patients to only sync most recent records...');

diff --git a/workflows/wf2/2-upsert-teis.js b/workflows/wf2/2-upsert-teis.js
@@ -6,18 +6,36 @@ fn(state => {
     O: 'prefer_not_to_answer',
   };
 
-  const DHIS2_PATIENT_NUMBER = '8d79403a-c2cc-11de-8d13-0010c6dffd0f';
-  const OPENMRS_AUTO_ID = '05a29f94-c0ed-11e2-94be-8c13b969e334';
+  const DHIS2_PATIENT_NUMBER = '8d79403a-c2cc-11de-8d13-0010c6dffd0f'; //DHIS2 ID or DHIS2 Patient Number
+  const OPENMRS_AUTO_ID = '05a29f94-c0ed-11e2-94be-8c13b969e334'; //MSF ID or OpenMRS Patient Number
   const patientsUpsert = [];
 
   const buildPatientsUpsert = (patient, isNewPatient) => {
     const dateCreated = patient.auditInfo.dateCreated.substring(0, 10);
 
-    const { identifier } =
-      patient.identifiers.find(
-        i => i.identifierType.uuid === DHIS2_PATIENT_NUMBER
-      ) ||
-      patient.identifiers.find(i => i.identifierType.uuid === OPENMRS_AUTO_ID);
+    function findIdentifierByUuid(identifiers, targetUuid) {
+      // Use the `find` method to locate the matching identifier
+      const matchingIdentifier = identifiers.find(
+        identifier => identifier.identifierType.uuid === targetUuid
+      );
+
+      // Return the `identifier` value if a match is found; otherwise, return null
+      return matchingIdentifier ? matchingIdentifier.identifier : undefined;
+    }
+
+    const calculateDOB = age => {
+      const currentDate = new Date();
+      const currentYear = currentDate.getFullYear();
+      const birthYear = currentYear - age;
+
+      const birthday = new Date(
+        birthYear,
+        currentDate.getMonth(),
+        currentDate.getDay()
+      );
+
+      return birthday.toISOString().replace(/\.\d+Z$/, '+0000');
+    };
 
     const enrollments = [
       {
@@ -31,33 +49,83 @@ fn(state => {
     const payload = {
       query: {
         ou: 'OPjuJMZFLop',
-        filter: [`AYbfTPYMNJH:Eq:${patient.uuid}`],
+        program: 'w9MSPn5oSqp',
+        filter: [`AYbfTPYMNJH:Eq:${patient.uuid}`], //upsert on omrs.patient.uid
       },
       data: {
         program: 'w9MSPn5oSqp',
         orgUnit: 'OPjuJMZFLop',
         trackedEntityType: 'cHlzCA2MuEF',
         attributes: [
           {
-            attribute: 'P4wdYGkldeG',
-            value: identifier,
+            attribute: 'fa7uwpCKIwa',
+            value: patient.person.names[0].givenName,
+          },
+          {
+            attribute: 'Jt9BhFZkvP2',
+            value: patient.person.names[0].familyName,
           },
           {
-            attribute: 'AYbfTPYMNJH',
+            attribute: 'P4wdYGkldeG', //DHIS2 ID ==> "Patient Number"
+            value: findIdentifierByUuid(
+              patient.identifiers,
+              DHIS2_PATIENT_NUMBER
+            ),
+          },
+          {
+            attribute: 'ZBoxuExmxcZ', //MSF ID ==> "OpenMRS Patient Number"
+            value: findIdentifierByUuid(patient.identifiers, OPENMRS_AUTO_ID),
+          },
+          {
+            attribute: 'AYbfTPYMNJH', //"OpenMRS Patient UID"
             value: patient.uuid,
           },
           {
             attribute: 'qptKDiv9uPl',
             value: genderOptions[patient.person.gender],
           },
           {
-            attribute: 'T1iX2NuPyqS',
+            attribute: 'Rv8WM2mTuS5',
             value: patient.person.age,
           },
+          {
+            attribute: 'WDp4nVor9Z7',
+            value: patient.person.birthdate,
+          },
+          // {
+          //   attribute: 'rBtrjV1Mqkz', //Place of living
+          //   value: patient.person.address,
+          // },
+          // {
+          //   attribute: 'Xvzc9e0JJmp', //nationality
+          //   value: patient.person.attributes[x].value, //input.attributeType = "24d1fa23-9778-4a8e-9f7b-93f694fc25e2"
+          // },
+          // {
+          //   attribute: 'YUIQIA2ClN6', //current status
+          //   value: patient.person.attributes[x].value, //input.attributeType = "e0b6ed99-72c4-4847-a442-e9929eac4a0f"
+          // },
+          // {
+          //   attribute: 'Qq6xQ2s6LO8', //legal status
+          //   value: patient.person.attributes[x].value, //input.attributeType = "a9b2c642-097f-43f8-b96b-4d2f50ffd9b1"
+          // },
+          // {
+          //   attribute: 'FpuGAOu6itZ', //marital status
+          //   value: patient.person.attributes[x].value, //input.attributeType = "3884dc76-c271-4bcb-8df8-81c6fb897f53"
+          // },
+          // {
+          //   attribute: 'v7k4OcXrWR8', //employment status
+          //   value: patient.person.attributes[x].value, //input.attributeType = "dd1f7f0f-ccea-4228-9aa8-a8c3b0ea4c3e"
+          // },
+          // {
+          //   attribute: 'SVoT2cVLd5O', //employment status
+          //   value: patient.person.attributes[x].value, //input.attributeType = "e363161a-9d5c-4331-8463-238938f018ed"
+          // },
         ],
       },
     };
 
+    console.log('mapped dhis2 payloads:: ', JSON.stringify(payload, null, 2));
+
     if (isNewPatient) {
       console.log('create enrollment');
       payload.data.enrollments = enrollments;
@@ -83,7 +151,8 @@ fn(async state => {
       'trackedEntityInstances',
       {
         ou: 'OPjuJMZFLop',
-        filter: [`jGNhqEeXy2L:Eq:${patient.uuid}`],
+        filter: [`AYbfTPYMNJH:Eq:${patient.uuid}`],
+        program: 'w9MSPn5oSqp',
       },
       {},
       state => {
@@ -106,12 +175,8 @@ fn(async state => {
 // Upsert TEIs to DHIS2
 each(
   'patientsUpsert[*]',
-  upsert(
-    'trackedEntityInstances',
-    state => state.data.query,
-    state => state.data.data
-  )
+  upsert('trackedEntityInstances', $.data.query, $.data.data)
 );
 
 // Clean up state
-fn(state => ({ ...state, data: {} }));
+fn(({ data, ...state }) => state);
diff --git a/workflows/wf2/3-get-encounters.js b/workflows/wf2/3-get-encounters.js
@@ -1,18 +1,24 @@
 // Fetch encounters from the date of cursor
 // OpenMRS demo instance does not support querying ALL records (q=all)
-getEncounters({ q: 'Patient', v: 'full', limit: 100 });
+// getEncounters({ q: 'Patient', v: 'full', limit: 100 });
+getEncounters({
+  q: 'Aisha',
+  v: 'full',
+  limit: 1,
+  encounterType: '95d68645-1b72-4290-be0b-ec1fb64bc067',
+});
 
 // Update cursor and return encounters
 fn(state => {
   const { cursor, data } = state;
-  console.log("cursor datetime::", cursor);
+  console.log('cursor datetime::', cursor);
 
   console.log('Filtering encounters to only get recent records...');
-  console.log(
-    'Encounters returned before we filter for most recent ::',
-    JSON.stringify(data, null, 2)
-  );
-  const encounters = data.body.results.filter(
+  // console.log(
+  //   'Encounters returned before we filter for most recent ::',
+  //   JSON.stringify(data, null, 2)
+  // );
+  const encounters = data.results.filter(
     encounter => encounter.encounterDatetime >= cursor
   );
   console.log('# of new encounters to sync to dhis2 ::', encounters.length);

diff --git a/workflows/wf2/4-get-oclmap.js b/workflows/wf2/4-get-oclmap.js
diff --git a/workflows/wf2/4-get-options-map.js b/workflows/wf2/4-get-options-map.js
@@ -0,0 +1,60 @@
+get(
+  'https://gist.githubusercontent.com/aleksa-krolls/b22987f7569bc069e963973401832349/raw/94ae98714c85a6e871fd2fb292c9bff5e324d3a1/msf_mhBaseline_optionsMap.json'
+);
+
+fn(state => {
+  state.optsMap = state.data;
+  // console.log(JSON.stringify(state.optsMap, null, 2), 'Options Map');
+  delete state.data;
+  delete state.references;
+  delete state.response;
+  return state;
+});
+
+fn(state => {
+  state.mhpssMap = {
+    dfdv3SkeXKe: 'a6c5188c-29f0-4d3d-8cf5-7852998df86f', //Has the patient attempted suicide or tried to kill themselves?
+    hWMBCCA2yy1: 'abede172-ba87-4ebe-8054-3afadb181ea3', //Is the patient currently at risk of hurting himself/herself or attempting suicide?
+    TWuCY5r2wx7: 'ccc4f06c-b76a-440d-9b7e-c48ba2c4a0ab', //Is the patient currently at risk of hurting others?
+    QHrIUMhjZlO: 'd516de07-979b-411c-b7e4-bd09cf7d9d91', //Does the patient regularly use alcohol / substances to become intoxicated?
+    H1fMCaOzr8F: '3e97c2d0-15c1-4cfd-884f-7a4721079217', //Has the patient experienced an act of aggression or violence?
+    yCwuZ0htrlH: '5f6e245c-83fc-421b-8d46-061ac773ae71', //Follow up session required?
+    RiiH9A53rvG: '6d3876be-0a27-466d-ad58-92edcc8c31fb', //Referral done
+    OZViJk8FPVd: 'c2664992-8a5a-4a6d-9238-5df591307d55', //Has the patient had thoughts of death or suicide?
+    qgfKPlIHjcD: 'd8c84af2-bd9b-4bf3-a815-81652cb0b0bc', //Patient experienced an act of aggression or violence - What type(s) of violence?
+    rSIazMFEBjD: '4dae5b12-070f-4153-b1ca-fbec906106e1', //Admission type
+    KSBMR1BDGwx: '1a8bf24f-4f36-4971-aad9-ae77f3525738', //Type of consultation
+    WDY6MkQWyHb: '722dd83a-c1cf-48ad-ac99-45ac131ccc96', //Consultation done by
+    AuDPJg6gZE7: '82978311-bef9-46f9-9a9a-cc62254b00a6', //Location of intervention
+    KeyiEPc4pII: '82978311-bef9-46f9-9a9a-cc62254b00a6', //Type of intervention
+    qfYPXP76j8g: 'c3c86c1b-07be-4506-ab25-8f35f4389b19', //Patient referred by
+    PCGI7EnvCQS: '45b39cbf-0fb2-4682-8544-8aaf3e07a744', //Current symptoms or complaints 1
+    RnbiVrrSFdm: 'ee1b7973-e931-494e-a9cb-22b814b4d8ed', //Current symptoms or complaints 2
+    CUdI1BJ5W8G: '92a92f62-3ff6-4944-9ea9-a7af23949bad', //Current symptoms or complaints 3
+    YfcNA5bvkxT: '9a8204ca-d908-4157-9285-7c970dbb5287', //Main category of symptoms
+    vC3bg9NwJ78: '3edcfddb-7988-4ce5-97a0-d4c46b267a04', //Duration of the main symptom
+    RqsvaPH9vHt: '22809b19-54ca-4d88-8d26-9577637c184e', //Clinical diagnosis
+    qacGXlyyQOS: 'a1a75011-0fef-460a-b666-dda2d171f39b', //CGI-S score
+    S22iy8o0iLg: 'aae000c3-5242-4e3c-bd1f-7e922a6d3d34', //Patient experienced an act of aggression or violence - Time between violence event and consultation
+    v0qFX0qv1tX: 'd5e3d927-f7ce-4fdd-ac4e-6ad0b510b608', //Main past or precipitating events - 1
+    SsQqwDBGxjh: '54a9b20e-bce5-4d4a-8c9c-e0248a182586', //Main past or precipitating events - 2
+    FLIlRjAwn4G: 'e0d4e006-85b5-41cb-8a21-e013b1978b8b', //Main past or precipitating events - 3
+    JUabDHhT1wJ: 'c1a3ed2d-6d9a-453d-9d93-749164a76413', //Main category of precipitating event
+    DlqJSA5VApl: '8fb3bb7d-c935-4b57-8444-1b953470e109', //Type of referral
+    DMaLm9u4GCq: 'b87a93ff-a4a1-4601-b35d-1e42bfa7e194', //Total number of beneficiaries in family consultation
+    CLGnlnFqqnk: '0a0c70d2-2ba5-4cb3-941f-b4a9a4a7ec6d', //Location of intervention - If Health Facility, specify
+    f64XCwzJW02: '41e68dee-a2a3-4e6c-9d96-53def5caff52', //Location of intervention - If MSF Health Facility, specify
+    YeaUNruqmca: '08cd4b4a-4b0b-4391-987b-b5b3d770d30f', //Location of intervention - If Mobile Clinic, specify
+    KjgDauY9v4J: 'e08d532b-e56c-43dc-b831-af705654d2dc', //Location of intervention - If other, specify
+    pj5hIE6iyAR: 'e08d532b-e56c-43dc-b831-af705654d2dc', //Current symptoms or complaints - If other, specify
+    pj5hIE6iyAR: 'e08d532b-e56c-43dc-b831-af705654d2dc', //Current symptoms or complaints - If other, specify
+    W7cPAi8iXLZ: '819f79e7-b9af-4afd-85d4-2ab677223113', //Clinical diagnosis - If other, specify
+    MF3RML0HLbP: 'b2c5b6e0-66f0-4b9d-8576-b6f48e0a06df', //MHOS score
+    m8qis4iUOTo: '790b41ce-e1e7-11e8-b02f-0242ac130002', //Past / Precipitating Events - If other, specify
+    //pN4iQH4AEzk: '722dd83a-c1cf-48ad-ac99-45ac131ccc96', //Consultation done by //TODO: Return BOOLEAN
+    //qptKDiv9uPl: 'ec42d68d-3e23-43de-b8c5-a03bb538e7c7', //Sex //TODO: Remove TEA?
+    //tsFOVnlc6lz: '5f3d618e-5c89-43bd-8c79-07e4e98c2f23', //PHQ9 Score //TODO: ass logic
+  };
+
+  return state;
+});