Merge branch 'master' into POC-560

app/amrs-3.x/amrs_id.js

@@ -0,0 +1,13 @@
+const axios = require('axios');
+try {
+  const formData = {
+    user: '1'
+  };
+  const formBody = querystring.stringify(formData);
+  request = await axios.post(
+    'https://ngx.ampath.or.ke/amrs-id-generator/generateidentifier',
+    formBody
+  );
+} catch (error) {
+  reply.response('Internal Server Error').code(500);
+}

app/lab-integration/utils/lab-client.js

@@ -69,6 +69,8 @@ export class LabClient {
         return this.postViralLoad(payload);
       case 3:
         return this.postCD4(payload);
+      case 5:
+        return this.postHPV(payload);
       default:
         break;
     }
@@ -84,20 +86,26 @@ export class LabClient {
   postCD4(payload) {
     return this.getPostRequest(payload, `${this.config.serverUrl}/api/cd4`);
   }
-
+  postHPV(payload) {
+    return this.getPostRequest(payload, `${this.config.serverUrl}/api/hpv`);
+  }
   getPostRequest(payload, endpoint) {
-    const options = {
-      uri: endpoint,
-      headers: {
-        apikey: this.config.apiKey,
-        'Content-Type': 'application/x-www-form-urlencoded'
-      },
-      method: 'POST',
-      // json: true,
-      form: payload,
-      timeout: 40000
-    };
-    return rp(options);
+    try {
+      const options = {
+        uri: endpoint,
+        headers: {
+          apikey: this.config.apiKey,
+          'Content-Type': 'application/x-www-form-urlencoded'
+        },
+        method: 'POST',
+        // json: true,
+        form: payload,
+        timeout: 40000
+      };
+      return rp(options);
+    } catch (error) {
+      console.log('getPostRequestError', error.message);
+    }
   }
 
   getFetchRequest(filterOptions, offset) {

app/lab-integration/utils/poc-eid-payload-helper.js

@@ -34,6 +34,17 @@
               amrs_location: getLocation(payload, 'mrsId')
             };
             break;
+          case 'HPV':
+            eidPayload = {
+              test: 5,
+              mflCode: getLocation(payload, 'mflCode'),
+              patient_identifier: payload.patientIdentifier,
+              dob: payload.birthDate,
+              order_no: payload.orderNumber,
+              datecollected: payload.dateDrawn,
+              sex: getGenderCode(payload.sex)
+            };
+            break;
           case 'DNAPCR':
             eidPayload = {
               test: 1,

app/otz/cohort-module.service.js

@@ -0,0 +1,54 @@
+var db = require('../../etl-db');
+
+export class CohortModuleService {
+  getCohortSummary = (cohortUuids) => {
+    const uuids = cohortUuids
+      .split(',')
+      .map((s) => {
+        return `"${s}"`;
+      })
+      .join(',');
+    return new Promise((resolve, reject) => {
+      let queryParts = {};
+      const sql = `SELECT 
+        c.uuid,
+        COUNT(DISTINCT cm.patient_id) AS total_patients,
+        IFNULL(SUM(CASE
+                    WHEN fl.hiv_viral_load < 200 THEN 1
+                    ELSE 0
+                END) / NULLIF(COUNT(DISTINCT cm.patient_id), 0) * 100,
+                0) AS suppression_rate_percentage
+    FROM
+        amrs.cohort c
+            LEFT JOIN
+        amrs.location l ON l.location_id = c.location_id
+            INNER JOIN
+        amrs.cohort_member cm ON c.cohort_id = cm.cohort_id
+            LEFT JOIN
+        (SELECT 
+            person_id, MAX(test_datetime) AS latest_test_datetime
+        FROM
+            etl.flat_labs_and_imaging
+        WHERE
+            hiv_viral_load IS NOT NULL
+        GROUP BY person_id) AS latest_tests ON cm.patient_id = latest_tests.person_id
+            LEFT JOIN
+        etl.flat_labs_and_imaging fl ON latest_tests.person_id = fl.person_id
+            AND latest_tests.latest_test_datetime = fl.test_datetime
+    WHERE
+        l.uuid = '${cohortUuids}'
+    GROUP BY c.cohort_id;
+    
+    `;
+
+      queryParts = {
+        sql: sql
+      };
+
+      return db.queryServer(queryParts, function (result) {
+        result.sql = sql;
+        resolve(result);
+      });
+    });
+  };
+}

app/reporting-framework/base-mysql.report.js

@@ -384,6 +384,63 @@ import * as txrtt_aggregate_report from './json-reports/tx-reports/tx-rtt/tx-rtt
 import * as txrtt_base_report from './json-reports/tx-reports/tx-rtt/tx-rtt-report-base.json';
 import * as txrtt_summary from './json-reports/txrtt-summary.json';
 
+//plhiv-ncd report
+import * as plhiv_ncd_v2_monthly_report from './json-reports/plhiv-ncd-v2-reports/plhiv-ncd-v2-report.json';
+
+import * as htn_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/hypertensive/htn-base.json';
+import * as htn_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/hypertensive/htn-aggregate.json';
+
+import * as dm_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/diabetic/dm-base.json';
+import * as dm_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/diabetic/dm-aggregate.json';
+
+import * as mh_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/mh-base.json';
+import * as mh_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/mh-aggregate.json';
+
+import * as dep_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/depressive-base.json';
+import * as dep_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/depressive-aggregate.json';
+
+import * as anx_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/anxiety-base.json';
+import * as anx_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/anxiety-aggregate.json';
+
+import * as bip_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/bipolar-and-related-mh-base.json';
+import * as bip_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/bipolar-and-related-mh-aggregate.json';
+
+import * as per_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/personality-mh-base.json';
+import * as per_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/personality-mh-aggregate.json';
+
+import * as fed_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/feeding-and-eating-mh-base.json';
+import * as fed_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/feeding-and-eating-mh-aggregate.json';
+
+import * as ocd_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/ocd-base.json';
+import * as ocd_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/ocd-aggregate.json';
+
+import * as genMD_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/general-mental-disorder-base.json';
+import * as genMD_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/general-mental-disorder-aggregate.json';
+
+import * as stMD_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/status-sub-total-base.json';
+import * as stMD_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/status-sub-total-aggregate.json';
+
+import * as totMD_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/total-mh-base.json';
+import * as totMD_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/mental-health-disorder/total-mh-aggregate.json';
+
+import * as cvd_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/cardiovascular-disease/cvd-base.json';
+import * as cvd_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/cardiovascular-disease/cvd-aggregate.json';
+
+import * as neu_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/neurological-disease/neuro-base.json';
+import * as neu_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/neurological-disease/neuro-aggregate.json';
+
+import * as rhe_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/rheumatologic-disease/rheu-base.json';
+import * as rhe_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/rheumatologic-disease/rheu-aggregate.json';
+
+import * as kd_plhiv_base from './json-reports/plhiv-ncd-v2-reports/disaggregations/kidney-disease/kd-base.json';
+import * as kd_plhiv_aggregate from './json-reports/plhiv-ncd-v2-reports/disaggregations/kidney-disease/kd-aggregate.json';
+//ahd report
+import * as ahd_monthly_summary from './json-reports/ahd_reports/ahd-monthly.json';
+import * as ahd_monthly_aggregate from './json-reports/ahd_reports/ahd-monthly-aggregate.json';
+import * as ahd_cohort_monthly_aggregate from './json-reports/ahd_reports/ahd-cohort-monthly-aggregate.json';
+import * as ahd_monthly_dataset_base from './json-reports/ahd_reports/ahd-monthly-dataset-base.json';
+import * as ahd_cohort_monthly_dataset_base from './json-reports/ahd_reports/ahd-cohort-monthly-dataset-base.json';
+import * as ahd_monthly_patient_list_template from './json-reports/ahd_reports/ahd_monthly_patient_list_template_post.json';
 export class BaseMysqlReport {
   constructor(reportName, params) {
     this.reportName = reportName;
@@ -977,6 +1034,40 @@ export class BaseMysqlReport {
             prepDatasetReport: this.cloneJsonSchema(prep_dataset_report)
           });
           break;
+        case 'ahd-monthly-summary':
+          resolve({
+            main: this.cloneJsonSchema(ahd_monthly_summary)
+          });
+          break;
+        case 'ahdMonthlySummaryReport':
+          resolve({
+            main: this.cloneJsonSchema(ahd_monthly_summary),
+            ahdMonthlyDataSetBase: this.cloneJsonSchema(
+              ahd_monthly_dataset_base
+            )
+          });
+          break;
+        case 'ahd-monthly-report-patient-list-template':
+          resolve({
+            main: this.cloneJsonSchema(ahd_monthly_patient_list_template)
+          });
+          break;
+        case 'ahdMonthlyAggregate':
+          resolve({
+            main: this.cloneJsonSchema(ahd_monthly_aggregate),
+            ahdMonthlyDataSetBase: this.cloneJsonSchema(
+              ahd_monthly_dataset_base
+            )
+          });
+          break;
+        case 'ahdCohortMonthlyAggregate':
+          resolve({
+            main: this.cloneJsonSchema(ahd_cohort_monthly_aggregate),
+            ahdCohortMonthlyDataSetBase: this.cloneJsonSchema(
+              ahd_cohort_monthly_dataset_base
+            )
+          });
+          break;
         case 'surgeBaselineReport':
           resolve({
             main: this.cloneJsonSchema(ltfu_surge_baseline_aggregate_report),
@@ -1795,6 +1886,107 @@ export class BaseMysqlReport {
             main: this.cloneJsonSchema(txrtt_summary)
           });
           break;
+        case 'plhiv-ncd-v2-monthly-report':
+          resolve({
+            main: this.cloneJsonSchema(plhiv_ncd_v2_monthly_report)
+          });
+          break;
+        case 'htnPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(htn_plhiv_aggregate),
+            htnPlhivBase: this.cloneJsonSchema(htn_plhiv_base)
+          });
+          break;
+        case 'dmPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(dm_plhiv_aggregate),
+            dmPlhivBase: this.cloneJsonSchema(dm_plhiv_base)
+          });
+          break;
+
+        case 'depPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(dep_plhiv_aggregate),
+            depPlhivBase: this.cloneJsonSchema(dep_plhiv_base)
+          });
+          break;
+
+        case 'anxPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(anx_plhiv_aggregate),
+            anxPlhivBase: this.cloneJsonSchema(anx_plhiv_base)
+          });
+          break;
+
+        case 'bipPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(bip_plhiv_aggregate),
+            bipPlhivBase: this.cloneJsonSchema(bip_plhiv_base)
+          });
+          break;
+
+        case 'perPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(per_plhiv_aggregate),
+            perPlhivBase: this.cloneJsonSchema(per_plhiv_base)
+          });
+          break;
+        case 'fedPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(fed_plhiv_aggregate),
+            fedPlhivBase: this.cloneJsonSchema(fed_plhiv_base)
+          });
+          break;
+
+        case 'ocdPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(ocd_plhiv_aggregate),
+            ocdPlhivBase: this.cloneJsonSchema(ocd_plhiv_base)
+          });
+          break;
+
+        case 'genMDPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(genMD_plhiv_aggregate),
+            genMDPlhivBase: this.cloneJsonSchema(genMD_plhiv_base)
+          });
+          break;
+        case 'stMDPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(stMD_plhiv_aggregate),
+            stMDPlhivBase: this.cloneJsonSchema(stMD_plhiv_base)
+          });
+          break;
+        case 'totMDPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(totMD_plhiv_aggregate),
+            totMDPlhivBase: this.cloneJsonSchema(totMD_plhiv_base)
+          });
+          break;
+        case 'cvdPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(cvd_plhiv_aggregate),
+            cvdPlhivBase: this.cloneJsonSchema(cvd_plhiv_base)
+          });
+          break;
+        case 'neuPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(neu_plhiv_aggregate),
+            neuPlhivBase: this.cloneJsonSchema(neu_plhiv_base)
+          });
+          break;
+        case 'rhePlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(rhe_plhiv_aggregate),
+            rhePlhivBase: this.cloneJsonSchema(rhe_plhiv_base)
+          });
+          break;
+        case 'kdPlhivAggregate':
+          resolve({
+            main: this.cloneJsonSchema(kd_plhiv_aggregate),
+            kdPlhivBase: this.cloneJsonSchema(kd_plhiv_base)
+          });
+          break;
         default:
           reject('Unknown report ', reportName);
           break;
@@ -1829,7 +2021,7 @@ export class BaseMysqlReport {
           });
         })
         .catch((error) => {
-          // console.error('Error Executing Mysql Query', error);
+          console.error('Error Executing Mysql Query', error);
           reject(error);
         });
     });

app/reporting-framework/hiv/moh-731.report.js

@@ -16,6 +16,8 @@ export class Moh731Report extends MultiDatasetPatientlistReport {
     params.hivMonthlyDatasetSource = 'etl.hiv_monthly_report_dataset_frozen'; // defaults to frozen
     params.hivVlDataSource =
       '(SELECT fli.person_id, fli.hiv_viral_load as vl_1, fli.test_datetime as vl_1_date FROM etl.flat_labs_and_imaging fli INNER JOIN (SELECT person_id, MAX(test_datetime) AS max_vl_1_date,max(encounter_id) as encounter_id FROM etl.flat_labs_and_imaging fli where fli.hiv_viral_load is not null GROUP BY person_id) max_dates ON fli.person_id = max_dates.person_id AND fli.test_datetime = max_dates.max_vl_1_date AND fli.encounter_id = max_dates.encounter_id)';
+    params.hivSummaryDataSource =
+      '(SELECT fhsvb.person_id, fhsvb.weight, fhsvb.height, fhsvb.cur_who_stage as stage FROM etl.flat_hiv_summary_v15b fhsvb where fhsvb.is_clinical_encounter = 1 and fhsvb.next_clinical_datetime_hiv is null)';
     console.log('creating new moh 731 report service');
     super(reportName, params);
   }